data_6MXF
#
_entry.id 6MXF
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.381
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 6MXF pdb_00006mxf 10.2210/pdb6mxf/pdb
WWPDB D_1000237739 ? ?
EMDB EMD-9292 ? ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.details
_pdbx_database_related.db_id
_pdbx_database_related.content_type
EMDB 'MicroED structure of thiostrepton at 1.9 A resolution' EMD-9292 'associated EM volume'
EMDB . EMD-9291 'other EM volume'
EMDB . EMD-9290 'other EM volume'
EMDB . EMD-9282 'other EM volume'
EMDB . EMD-9283 'other EM volume'
EMDB . EMD-9284 'other EM volume'
EMDB . EMD-9285 'other EM volume'
EMDB . EMD-9286 'other EM volume'
EMDB . EMD-9287 'other EM volume'
EMDB . EMD-9288 'other EM volume'
EMDB . EMD-9289 'other EM volume'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 6MXF
_pdbx_database_status.recvd_initial_deposition_date 2018-10-30
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Jones, C.G.' 1 0000-0003-4308-1368
'Martynowycz, M.W.' 2 0000-0003-0055-230X
'Hattne, J.' 3 0000-0002-8936-0912
'Fulton, T.' 4 ?
'Stoltz, B.M.' 5 0000-0001-9837-1528
'Rodriguez, J.A.' 6 0000-0001-8471-2504
'Nelson, H.M.' 7 0000-0002-4666-2793
'Gonen, T.' 8 0000-0002-9254-4069
#
_citation.abstract ?
_citation.abstract_id_CAS ?
_citation.book_id_ISBN ?
_citation.book_publisher ?
_citation.book_publisher_city ?
_citation.book_title ?
_citation.coordinate_linkage ?
_citation.country US
_citation.database_id_Medline ?
_citation.details ?
_citation.id primary
_citation.journal_abbrev 'ACS Cent Sci'
_citation.journal_id_ASTM ?
_citation.journal_id_CSD ?
_citation.journal_id_ISSN 2374-7943
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume 4
_citation.language ?
_citation.page_first 1587
_citation.page_last 1592
_citation.title 'The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination.'
_citation.year 2018
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1021/acscentsci.8b00760
_citation.pdbx_database_id_PubMed 30555912
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Jones, C.G.' 1 ?
primary 'Martynowycz, M.W.' 2 ?
primary 'Hattne, J.' 3 ?
primary 'Fulton, T.J.' 4 ?
primary 'Stoltz, B.M.' 5 ?
primary 'Rodriguez, J.A.' 6 ?
primary 'Nelson, H.M.' 7 ?
primary 'Gonen, T.' 8 ?
#
_cell.angle_alpha 90.00
_cell.angle_alpha_esd ?
_cell.angle_beta 90.00
_cell.angle_beta_esd ?
_cell.angle_gamma 90.00
_cell.angle_gamma_esd ?
_cell.entry_id 6MXF
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 26.219
_cell.length_a_esd ?
_cell.length_b 26.219
_cell.length_b_esd ?
_cell.length_c 27.534
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB 8
_cell.reciprocal_angle_alpha ?
_cell.reciprocal_angle_beta ?
_cell.reciprocal_angle_gamma ?
_cell.reciprocal_angle_alpha_esd ?
_cell.reciprocal_angle_beta_esd ?
_cell.reciprocal_angle_gamma_esd ?
_cell.reciprocal_length_a ?
_cell.reciprocal_length_b ?
_cell.reciprocal_length_c ?
_cell.reciprocal_length_a_esd ?
_cell.reciprocal_length_b_esd ?
_cell.reciprocal_length_c_esd ?
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 6MXF
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 96
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 43 21 2'
_symmetry.pdbx_full_space_group_name_H-M ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn Thiostrepton 1805.985 1 ? ? ? ?
2 water nat water 18.015 2 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code '(QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)'
_entity_poly.pdbx_seq_one_letter_code_can XIASASCTTCICTCSCSSX
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 QUA n
1 2 ILE n
1 3 ALA n
1 4 DHA n
1 5 ALA n
1 6 SER n
1 7 BB9 n
1 8 THR n
1 9 DBU n
1 10 DCY n
1 11 TS9 n
1 12 BB9 n
1 13 THR n
1 14 BB9 n
1 15 MH6 n
1 16 BB9 n
1 17 DHA n
1 18 DHA n
1 19 NH2 n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num 1
_pdbx_entity_src_syn.pdbx_end_seq_num 19
_pdbx_entity_src_syn.organism_scientific 'Streptomyces azureus'
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 146537
_pdbx_entity_src_syn.details ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 6MXF
_struct_ref.pdbx_db_accession 6MXF
_struct_ref.pdbx_db_isoform ?
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin 1
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 6MXF
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 1
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 19
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 6MXF
_struct_ref_seq.db_align_beg 0
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 18
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 0
_struct_ref_seq.pdbx_auth_seq_align_end 18
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093
BB9 'peptide linking' n '(2Z)-2-amino-3-sulfanylprop-2-enoic acid' ? 'C3 H5 N O2 S' 119.142
DBU 'peptide linking' n '(2Z)-2-AMINOBUT-2-ENOIC ACID' Z-DEHYDROBUTYRINE 'C4 H7 N O2' 101.104
DCY 'D-peptide linking' . D-CYSTEINE ? 'C3 H7 N O2 S' 121.158
DHA 'peptide linking' n '2-AMINO-ACRYLIC ACID' 2,3-DIDEHYDROALANINE 'C3 H5 N O2' 87.077
HOH non-polymer . WATER ? 'H2 O' 18.015
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173
MH6 'peptide linking' n '3-hydroxy-2-iminopropanoic acid' ? 'C3 H5 N O3' 103.077
NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023
QUA non-polymer . '8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID' ? 'C12 H13 N O4' 235.236
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119
TS9 'L-peptide linking' n '(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid' ? 'C6 H13 N O4' 163.172
#
_exptl.absorpt_coefficient_mu ?
_exptl.absorpt_correction_T_max ?
_exptl.absorpt_correction_T_min ?
_exptl.absorpt_correction_type ?
_exptl.absorpt_process_details ?
_exptl.entry_id 6MXF
_exptl.crystals_number ?
_exptl.details ?
_exptl.method 'ELECTRON CRYSTALLOGRAPHY'
_exptl.method_details ?
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews ?
_exptl_crystal.density_percent_sol ?
_exptl_crystal.description ?
_exptl_crystal.preparation ?
#
_diffrn.id 1
_diffrn.ambient_temp ?
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
_diffrn.pdbx_serial_crystal_experiment ?
#
_diffrn_detector.area_resol_mean ?
_diffrn_detector.details ?
_diffrn_detector.detector ?
_diffrn_detector.diffrn_id 1
_diffrn_detector.dtime ?
_diffrn_detector.pdbx_collection_date 2018-10-03
_diffrn_detector.pdbx_collection_time_total ?
_diffrn_detector.pdbx_frames_total ?
_diffrn_detector.pdbx_frequency ?
_diffrn_detector.type ?
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.0251
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.current ?
_diffrn_source.details ?
_diffrn_source.diffrn_id 1
_diffrn_source.pdbx_synchrotron_beamline ?
_diffrn_source.pdbx_synchrotron_site ?
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 0.0251
_diffrn_source.power ?
_diffrn_source.size ?
_diffrn_source.source ?
_diffrn_source.take-off_angle ?
_diffrn_source.target ?
_diffrn_source.type ?
_diffrn_source.voltage ?
#
_reflns.B_iso_Wilson_estimate ?
_reflns.Friedel_coverage ?
_reflns.R_free_details ?
_reflns.Rmerge_F_all ?
_reflns.Rmerge_F_obs ?
_reflns.d_resolution_high 1.90
_reflns.d_resolution_low 18.99
_reflns.data_reduction_details ?
_reflns.data_reduction_method ?
_reflns.details ?
_reflns.entry_id 6MXF
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.number_all ?
_reflns.number_gt ?
_reflns.number_obs 686
_reflns.observed_criterion ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.observed_criterion_I_max ?
_reflns.observed_criterion_I_min ?
_reflns.observed_criterion_sigma_F ?
_reflns.observed_criterion_sigma_I ?
_reflns.pdbx_CC_half 0.985
_reflns.pdbx_R_split ?
_reflns.pdbx_Rmerge_I_all ?
_reflns.pdbx_Rmerge_I_obs 0.236
_reflns.pdbx_Rpim_I_all 0.084
_reflns.pdbx_Rrim_I_all 0.251
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_d_opt ?
_reflns.pdbx_d_res_high_opt ?
_reflns.pdbx_d_res_low_opt ?
_reflns.pdbx_d_res_opt_method ?
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_netI_over_av_sigmaI ?
_reflns.pdbx_netI_over_sigmaI 5.1
_reflns.pdbx_number_measured_all ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_redundancy 8.1
_reflns.pdbx_res_netI_over_av_sigmaI_2 ?
_reflns.pdbx_res_netI_over_sigmaI_2 ?
_reflns.pdbx_scaling_rejects ?
_reflns.percent_possible_obs 78.6
_reflns.phase_calculation_details ?
_reflns.threshold_expression ?
#
_reflns_shell.d_res_high 1.90
_reflns_shell.d_res_low 2.13
_reflns_shell.meanI_over_sigI_all ?
_reflns_shell.meanI_over_sigI_obs 3.4
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_possible ?
_reflns_shell.number_unique_all 93
_reflns_shell.number_unique_obs ?
_reflns_shell.percent_possible_all 40.3
_reflns_shell.percent_possible_obs ?
_reflns_shell.Rmerge_F_all ?
_reflns_shell.Rmerge_F_obs ?
_reflns_shell.Rmerge_I_all ?
_reflns_shell.Rmerge_I_obs 0.32
_reflns_shell.meanI_over_sigI_gt ?
_reflns_shell.meanI_over_uI_all ?
_reflns_shell.meanI_over_uI_gt ?
_reflns_shell.number_measured_gt ?
_reflns_shell.number_unique_gt ?
_reflns_shell.percent_possible_gt ?
_reflns_shell.Rmerge_F_gt ?
_reflns_shell.Rmerge_I_gt ?
_reflns_shell.pdbx_redundancy 4.9
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.pdbx_chi_squared ?
_reflns_shell.pdbx_netI_over_sigmaI_all ?
_reflns_shell.pdbx_netI_over_sigmaI_obs ?
_reflns_shell.pdbx_Rrim_I_all ?
_reflns_shell.pdbx_Rpim_I_all ?
_reflns_shell.pdbx_rejects ?
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id ?
_reflns_shell.pdbx_CC_half 0.813
_reflns_shell.pdbx_R_split ?
#
_refine.aniso_B[1][1] 0.18
_refine.aniso_B[1][2] -0.00
_refine.aniso_B[1][3] -0.00
_refine.aniso_B[2][2] 0.18
_refine.aniso_B[2][3] -0.00
_refine.aniso_B[3][3] -0.37
_refine.B_iso_max ?
_refine.B_iso_mean 6.811
_refine.B_iso_min ?
_refine.correlation_coeff_Fo_to_Fc 0.931
_refine.correlation_coeff_Fo_to_Fc_free 0.940
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS'
_refine.diff_density_max ?
_refine.diff_density_max_esd ?
_refine.diff_density_min ?
_refine.diff_density_min_esd ?
_refine.diff_density_rms ?
_refine.diff_density_rms_esd ?
_refine.entry_id 6MXF
_refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY'
_refine.ls_abs_structure_details ?
_refine.ls_abs_structure_Flack ?
_refine.ls_abs_structure_Flack_esd ?
_refine.ls_abs_structure_Rogers ?
_refine.ls_abs_structure_Rogers_esd ?
_refine.ls_d_res_high 1.91
_refine.ls_d_res_low 18.99
_refine.ls_extinction_coef ?
_refine.ls_extinction_coef_esd ?
_refine.ls_extinction_expression ?
_refine.ls_extinction_method ?
_refine.ls_goodness_of_fit_all ?
_refine.ls_goodness_of_fit_all_esd ?
_refine.ls_goodness_of_fit_obs ?
_refine.ls_goodness_of_fit_obs_esd ?
_refine.ls_hydrogen_treatment ?
_refine.ls_matrix_type ?
_refine.ls_number_constraints ?
_refine.ls_number_parameters ?
_refine.ls_number_reflns_all ?
_refine.ls_number_reflns_obs 620
_refine.ls_number_reflns_R_free 57
_refine.ls_number_reflns_R_work ?
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 78.18
_refine.ls_percent_reflns_R_free 8.4
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs 0.19276
_refine.ls_R_factor_R_free 0.21798
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work 0.19046
_refine.ls_R_Fsqd_factor_obs ?
_refine.ls_R_I_factor_obs ?
_refine.ls_redundancy_reflns_all ?
_refine.ls_redundancy_reflns_obs ?
_refine.ls_restrained_S_all ?
_refine.ls_restrained_S_obs ?
_refine.ls_shift_over_esd_max ?
_refine.ls_shift_over_esd_mean ?
_refine.ls_structure_factor_coef ?
_refine.ls_weighting_details ?
_refine.ls_weighting_scheme ?
_refine.ls_wR_factor_all ?
_refine.ls_wR_factor_obs ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.occupancy_max ?
_refine.occupancy_min ?
_refine.solvent_model_details ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.ls_R_factor_gt ?
_refine.ls_goodness_of_fit_gt ?
_refine.ls_goodness_of_fit_ref ?
_refine.ls_shift_over_su_max ?
_refine.ls_shift_over_su_max_lt ?
_refine.ls_shift_over_su_mean ?
_refine.ls_shift_over_su_mean_lt ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F ?
_refine.pdbx_ls_sigma_Fsqd ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_starting_model 1e9w
_refine.pdbx_stereochemistry_target_values ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_overall_ESU_R 0.352
_refine.pdbx_overall_ESU_R_Free 0.202
_refine.pdbx_solvent_vdw_probe_radii 1.20
_refine.pdbx_solvent_ion_probe_radii 0.80
_refine.pdbx_solvent_shrinkage_radii 0.80
_refine.pdbx_real_space_R ?
_refine.pdbx_density_correlation ?
_refine.pdbx_pd_number_of_powder_patterns ?
_refine.pdbx_pd_number_of_points ?
_refine.pdbx_pd_meas_number_of_points ?
_refine.pdbx_pd_proc_ls_prof_R_factor ?
_refine.pdbx_pd_proc_ls_prof_wR_factor ?
_refine.pdbx_pd_Marquardt_correlation_coeff ?
_refine.pdbx_pd_Fsqrd_R_factor ?
_refine.pdbx_pd_ls_matrix_band_width ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.pdbx_diffrn_id 1
_refine.overall_SU_B 3.282
_refine.overall_SU_ML 0.098
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_average_fsc_overall ?
_refine.pdbx_average_fsc_work ?
_refine.pdbx_average_fsc_free ?
#
_refine_hist.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY'
_refine_hist.cycle_id 1
_refine_hist.pdbx_number_atoms_protein ?
_refine_hist.pdbx_number_atoms_nucleic_acid ?
_refine_hist.pdbx_number_atoms_ligand ?
_refine_hist.number_atoms_solvent ?
_refine_hist.number_atoms_total 116
_refine_hist.d_res_high .
_refine_hist.d_res_low .
#
loop_
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.criterion
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.number
_refine_ls_restr.rejects
_refine_ls_restr.type
_refine_ls_restr.weight
_refine_ls_restr.pdbx_restraint_function
'ELECTRON CRYSTALLOGRAPHY' ? 0.015 0.017 123 ? r_bond_refined_d ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.025 0.018 107 ? r_bond_other_d ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 2.760 2.241 120 ? r_angle_refined_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 1.374 2.283 213 ? r_angle_other_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 3.623 5.000 3 ? r_dihedral_angle_1_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_dihedral_angle_2_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 7.901 15.000 4 ? r_dihedral_angle_3_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_dihedral_angle_4_deg ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.062 0.200 15 ? r_chiral_restr ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.010 0.020 135 ? r_gen_planes_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.003 0.020 49 ? r_gen_planes_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_nbd_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_nbd_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_nbtor_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_nbtor_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_xyhbond_nbd_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_xyhbond_nbd_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_metal_ion_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_metal_ion_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_vdw_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_vdw_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_hbond_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_hbond_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_symmetry_metal_ion_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.625 0.798 62 ? r_mcbond_it ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.620 0.810 63 ? r_mcbond_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.893 1.194 37 ? r_mcangle_it ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.881 1.223 38 ? r_mcangle_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.609 0.743 60 ? r_scbond_it ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.604 0.754 61 ? r_scbond_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_scangle_it ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 0.892 1.161 84 ? r_scangle_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 1.546 10.960 101 ? r_long_range_B_refined ? ?
'ELECTRON CRYSTALLOGRAPHY' ? 1.539 10.959 102 ? r_long_range_B_other ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_rigid_bond_restr ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_sphericity_free ? ?
'ELECTRON CRYSTALLOGRAPHY' ? ? ? ? ? r_sphericity_bonded ? ?
#
_refine_ls_shell.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY'
_refine_ls_shell.d_res_high 1.915
_refine_ls_shell.d_res_low 1.964
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.number_reflns_R_free 0
_refine_ls_shell.number_reflns_R_work 2
_refine_ls_shell.percent_reflns_obs 3.33
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.R_factor_obs ?
_refine_ls_shell.R_factor_R_free 0.000
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.R_factor_R_work 0.182
_refine_ls_shell.redundancy_reflns_all ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.wR_factor_all ?
_refine_ls_shell.wR_factor_obs ?
_refine_ls_shell.wR_factor_R_free ?
_refine_ls_shell.wR_factor_R_work ?
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.pdbx_phase_error ?
_refine_ls_shell.pdbx_fsc_work ?
_refine_ls_shell.pdbx_fsc_free ?
#
_struct.entry_id 6MXF
_struct.title 'MicroED structure of thiostrepton at 1.9 A resolution'
_struct.pdbx_model_details ?
_struct.pdbx_formula_weight ?
_struct.pdbx_formula_weight_method ?
_struct.pdbx_model_type_details ?
_struct.pdbx_CASP_flag N
#
_struct_keywords.entry_id 6MXF
_struct_keywords.text ANTIBIOTIC
_struct_keywords.pdbx_keywords ANTIBIOTIC
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale both ? A QUA 1 C7 ? ? ? 1_555 A ILE 2 N ? ? A QUA 0 A ILE 1 1_555 ? ? ? ? ? ? ? 1.547 ? ?
covale2 covale one ? A QUA 1 C11 ? ? ? 1_555 A THR 13 OG1 ? ? A QUA 0 A THR 12 1_555 ? ? ? ? ? ? ? 1.307 ? ?
covale3 covale both ? A ALA 3 C ? ? ? 1_555 A DHA 4 N ? ? A ALA 2 A DHA 3 1_555 ? ? ? ? ? ? ? 1.349 ? ?
covale4 covale both ? A DHA 4 C ? ? ? 1_555 A ALA 5 N ? ? A DHA 3 A ALA 4 1_555 ? ? ? ? ? ? ? 1.424 ? ?
covale5 covale both ? A SER 6 C ? ? ? 1_555 A BB9 7 N ? ? A SER 5 A BB9 6 1_555 ? ? ? ? ? ? ? 1.343 ? ?
covale6 covale one ? A SER 6 C ? ? ? 1_555 A BB9 7 SG ? ? A SER 5 A BB9 6 1_555 ? ? ? ? ? ? ? 1.722 ? ?
covale7 covale one ? A SER 6 CA ? ? ? 1_555 A BB9 14 C ? ? A SER 5 A BB9 13 1_555 ? ? ? ? ? ? ? 1.512 ? ?
covale8 covale one ? A SER 6 CB ? ? ? 1_555 A MH6 15 CB ? ? A SER 5 A MH6 14 1_555 ? ? ? ? ? ? ? 1.578 ? ?
covale9 covale both ? A BB9 7 C ? ? ? 1_555 A THR 8 N ? ? A BB9 6 A THR 7 1_555 ? ? ? ? ? ? ? 1.422 ? ?
covale10 covale both ? A THR 8 C ? ? ? 1_555 A DBU 9 N ? ? A THR 7 A DBU 8 1_555 ? ? ? ? ? ? ? 1.356 ? ?
covale11 covale one ? A DBU 9 C ? ? ? 1_555 A DCY 10 SG ? ? A DBU 8 A DCY 9 1_555 ? ? ? ? ? ? ? 1.719 ? ?
covale12 covale both ? A DBU 9 C ? ? ? 1_555 A DCY 10 N ? ? A DBU 8 A DCY 9 1_555 ? ? ? ? ? ? ? 1.414 ? ?
covale13 covale both ? A DCY 10 C ? ? ? 1_555 A TS9 11 N ? ? A DCY 9 A TS9 10 1_555 ? ? ? ? ? ? ? 1.345 ? ?
covale14 covale one ? A TS9 11 C ? ? ? 1_555 A BB9 12 SG ? ? A TS9 10 A BB9 11 1_555 ? ? ? ? ? ? ? 1.709 ? ?
covale15 covale both ? A TS9 11 C ? ? ? 1_555 A BB9 12 N ? ? A TS9 10 A BB9 11 1_555 ? ? ? ? ? ? ? 1.330 ? ?
covale16 covale both ? A BB9 12 C ? ? ? 1_555 A THR 13 N ? ? A BB9 11 A THR 12 1_555 ? ? ? ? ? ? ? 1.394 ? ?
covale17 covale one ? A THR 13 C ? ? ? 1_555 A BB9 14 SG ? ? A THR 12 A BB9 13 1_555 ? ? ? ? ? ? ? 1.712 ? ?
covale18 covale both ? A THR 13 C ? ? ? 1_555 A BB9 14 N ? ? A THR 12 A BB9 13 1_555 ? ? ? ? ? ? ? 1.326 ? ?
covale19 covale both ? A BB9 14 C ? ? ? 1_555 A MH6 15 N ? ? A BB9 13 A MH6 14 1_555 ? ? ? ? ? ? ? 1.379 ? ?
covale20 covale both ? A MH6 15 C ? ? ? 1_555 A BB9 16 N ? ? A MH6 14 A BB9 15 1_555 ? ? ? ? ? ? ? 1.340 ? ?
covale21 covale one ? A MH6 15 C ? ? ? 1_555 A BB9 16 SG ? ? A MH6 14 A BB9 15 1_555 ? ? ? ? ? ? ? 1.678 ? ?
covale22 covale both ? A BB9 16 C ? ? ? 1_555 A DHA 17 N ? ? A BB9 15 A DHA 16 1_555 ? ? ? ? ? ? ? 1.337 ? ?
covale23 covale both ? A DHA 17 C ? ? ? 1_555 A DHA 18 N ? ? A DHA 16 A DHA 17 1_555 ? ? ? ? ? ? ? 1.385 ? ?
covale24 covale both ? A DHA 18 C ? ? ? 1_555 A NH2 19 N ? ? A DHA 17 A NH2 18 1_555 ? ? ? ? ? ? ? 1.282 ? ?
#
_struct_conn_type.id covale
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
_struct_site.id AC1
_struct_site.pdbx_evidence_code Software
_struct_site.pdbx_auth_asym_id A
_struct_site.pdbx_auth_comp_id QUA
_struct_site.pdbx_auth_seq_id 0
_struct_site.pdbx_auth_ins_code ?
_struct_site.pdbx_num_residues 2
_struct_site.details 'binding site for THIOSTREPTON chain A'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 2 HOH B . ? HOH A 101 . ? 1_555 ?
2 AC1 2 HOH B . ? HOH A 102 . ? 1_555 ?
#
_atom_sites.entry_id 6MXF
_atom_sites.fract_transf_matrix[1][1] 0.038140
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] -0.000000
_atom_sites.fract_transf_matrix[2][2] 0.038140
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] -0.000000
_atom_sites.fract_transf_matrix[3][3] 0.036319
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
loop_
_atom_type.symbol
C
N
O
S
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O12 . QUA A 1 1 ? 10.846 5.950 -3.568 1.00 5.38 ? 0 QUA A O12 1
HETATM 2 C C11 . QUA A 1 1 ? 9.756 5.430 -3.418 1.00 5.55 ? 0 QUA A C11 1
HETATM 3 C C2 . QUA A 1 1 ? 9.569 3.950 -3.605 1.00 6.27 ? 0 QUA A C2 1
HETATM 4 N N1 . QUA A 1 1 ? 8.323 3.479 -3.469 1.00 6.37 ? 0 QUA A N1 1
HETATM 5 C C3 . QUA A 1 1 ? 10.644 3.163 -3.979 1.00 6.46 ? 0 QUA A C3 1
HETATM 6 C C9 . QUA A 1 1 ? 8.090 2.191 -3.746 1.00 6.39 ? 0 QUA A C9 1
HETATM 7 C C4 . QUA A 1 1 ? 10.418 1.813 -4.212 1.00 6.67 ? 0 QUA A C4 1
HETATM 8 C C8 . QUA A 1 1 ? 6.630 1.779 -3.753 1.00 6.46 ? 0 QUA A C8 1
HETATM 9 C C10 . QUA A 1 1 ? 9.113 1.302 -4.110 1.00 6.56 ? 0 QUA A C10 1
HETATM 10 O O16 . QUA A 1 1 ? 6.068 1.903 -5.062 1.00 6.25 ? 0 QUA A O16 1
HETATM 11 C C7 . QUA A 1 1 ? 6.526 0.325 -3.301 1.00 6.74 ? 0 QUA A C7 1
HETATM 12 C C13 . QUA A 1 1 ? 11.569 0.863 -4.484 1.00 6.78 ? 0 QUA A C13 1
HETATM 13 O O15 . QUA A 1 1 ? 12.634 1.475 -5.206 1.00 7.06 ? 0 QUA A O15 1
HETATM 14 C C5 . QUA A 1 1 ? 8.784 -0.089 -4.285 1.00 6.50 ? 0 QUA A C5 1
HETATM 15 C C14 . QUA A 1 1 ? 12.092 0.266 -3.210 1.00 6.98 ? 0 QUA A C14 1
HETATM 16 C C6 . QUA A 1 1 ? 7.570 -0.536 -3.956 1.00 6.51 ? 0 QUA A C6 1
ATOM 17 N N . ILE A 1 2 ? 6.536 -0.046 -1.799 1.00 7.73 ? 1 ILE A N 1
ATOM 18 C CA . ILE A 1 2 ? 5.563 0.737 -0.968 1.00 7.86 ? 1 ILE A CA 1
ATOM 19 C C . ILE A 1 2 ? 6.255 1.917 -0.265 1.00 7.83 ? 1 ILE A C 1
ATOM 20 O O . ILE A 1 2 ? 5.548 2.757 0.275 1.00 7.34 ? 1 ILE A O 1
ATOM 21 C CB . ILE A 1 2 ? 4.846 -0.166 0.056 1.00 8.34 ? 1 ILE A CB 1
ATOM 22 C CG1 . ILE A 1 2 ? 5.850 -0.751 1.058 1.00 8.54 ? 1 ILE A CG1 1
ATOM 23 C CG2 . ILE A 1 2 ? 4.004 -1.220 -0.650 1.00 8.28 ? 1 ILE A CG2 1
ATOM 24 C CD1 . ILE A 1 2 ? 5.230 -1.487 2.230 1.00 8.80 ? 1 ILE A CD1 1
ATOM 25 N N . ALA A 1 3 ? 7.586 1.945 -0.214 1.00 7.97 ? 2 ALA A N 1
ATOM 26 C CA . ALA A 1 3 ? 8.348 3.093 0.318 1.00 8.02 ? 2 ALA A CA 1
ATOM 27 C C . ALA A 1 3 ? 9.792 3.023 -0.191 1.00 7.48 ? 2 ALA A C 1
ATOM 28 O O . ALA A 1 3 ? 10.206 1.927 -0.550 1.00 7.19 ? 2 ALA A O 1
ATOM 29 C CB . ALA A 1 3 ? 8.293 3.122 1.823 1.00 8.08 ? 2 ALA A CB 1
HETATM 30 N N . DHA A 1 4 ? 10.440 4.201 -0.080 1.00 6.39 ? 3 DHA A N 1
HETATM 31 C CA . DHA A 1 4 ? 11.606 4.576 -0.640 1.00 6.07 ? 3 DHA A CA 1
HETATM 32 C CB . DHA A 1 4 ? 12.572 3.701 -0.913 1.00 5.81 ? 3 DHA A CB 1
HETATM 33 C C . DHA A 1 4 ? 11.707 6.012 -0.922 1.00 5.70 ? 3 DHA A C 1
HETATM 34 O O . DHA A 1 4 ? 10.688 6.662 -0.582 1.00 5.67 ? 3 DHA A O 1
ATOM 35 N N . ALA A 1 5 ? 12.950 6.615 -1.269 1.00 5.17 ? 4 ALA A N 1
ATOM 36 C CA . ALA A 1 5 ? 13.040 7.928 -1.954 1.00 5.05 ? 4 ALA A CA 1
ATOM 37 C C . ALA A 1 5 ? 13.658 7.730 -3.347 1.00 5.05 ? 4 ALA A C 1
ATOM 38 O O . ALA A 1 5 ? 14.744 7.150 -3.427 1.00 4.98 ? 4 ALA A O 1
ATOM 39 C CB . ALA A 1 5 ? 13.860 8.885 -1.122 1.00 5.08 ? 4 ALA A CB 1
ATOM 40 N N . SER A 1 6 ? 13.019 8.291 -4.380 1.00 5.06 ? 5 SER A N 1
ATOM 41 C CA . SER A 1 6 ? 13.428 8.204 -5.807 1.00 5.18 ? 5 SER A CA 1
ATOM 42 C C . SER A 1 6 ? 13.368 6.747 -6.304 1.00 5.10 ? 5 SER A C 1
ATOM 43 C CB . SER A 1 6 ? 14.812 8.807 -5.984 1.00 5.63 ? 5 SER A CB 1
HETATM 44 N N . BB9 A 1 7 ? 12.292 6.028 -6.664 1.00 4.98 ? 6 BB9 A N 1
HETATM 45 C CA . BB9 A 1 7 ? 12.535 4.769 -7.023 1.00 5.01 ? 6 BB9 A CA 1
HETATM 46 C C . BB9 A 1 7 ? 11.542 3.868 -7.573 1.00 4.99 ? 6 BB9 A C 1
HETATM 47 O O . BB9 A 1 7 ? 11.628 2.663 -7.295 1.00 4.90 ? 6 BB9 A O 1
HETATM 48 C CB . BB9 A 1 7 ? 13.785 4.396 -6.782 1.00 5.16 ? 6 BB9 A CB 1
HETATM 49 S SG . BB9 A 1 7 ? 14.688 5.664 -6.084 1.00 5.00 ? 6 BB9 A SG 1
ATOM 50 N N . THR A 1 8 ? 10.301 4.501 -7.857 1.00 5.32 ? 7 THR A N 1
ATOM 51 C CA . THR A 1 8 ? 9.102 3.767 -8.259 1.00 5.40 ? 7 THR A CA 1
ATOM 52 C C . THR A 1 8 ? 8.444 4.551 -9.398 1.00 5.72 ? 7 THR A C 1
ATOM 53 O O . THR A 1 8 ? 8.763 5.760 -9.558 1.00 5.34 ? 7 THR A O 1
ATOM 54 C CB . THR A 1 8 ? 8.206 3.517 -7.033 1.00 5.43 ? 7 THR A CB 1
ATOM 55 O OG1 . THR A 1 8 ? 7.218 2.536 -7.355 1.00 5.43 ? 7 THR A OG1 1
ATOM 56 C CG2 . THR A 1 8 ? 7.506 4.766 -6.534 1.00 5.56 ? 7 THR A CG2 1
HETATM 57 N N . DBU A 1 9 ? 7.345 4.161 -10.090 1.00 6.64 ? 8 DBU A N 1
HETATM 58 C CA . DBU A 1 9 ? 6.567 4.862 -10.920 1.00 6.72 ? 8 DBU A CA 1
HETATM 59 C CB . DBU A 1 9 ? 7.054 5.379 -12.070 1.00 7.02 ? 8 DBU A CB 1
HETATM 60 C CG . DBU A 1 9 ? 8.490 5.160 -12.530 1.00 7.08 ? 8 DBU A CG 1
HETATM 61 C C . DBU A 1 9 ? 5.153 5.100 -10.618 1.00 7.34 ? 8 DBU A C 1
HETATM 62 N N . DCY A 1 10 ? 4.604 4.402 -9.518 1.00 8.16 ? 9 DCY A N 1
HETATM 63 C CA . DCY A 1 10 ? 3.163 4.403 -9.614 1.00 8.49 ? 9 DCY A CA 1
HETATM 64 C C . DCY A 1 10 ? 2.485 4.728 -8.275 1.00 9.26 ? 9 DCY A C 1
HETATM 65 O O . DCY A 1 10 ? 1.240 4.758 -8.286 1.00 9.42 ? 9 DCY A O 1
HETATM 66 C CB . DCY A 1 10 ? 2.775 5.393 -10.698 1.00 8.31 ? 9 DCY A CB 1
HETATM 67 S SG . DCY A 1 10 ? 4.103 5.543 -11.905 1.00 7.60 ? 9 DCY A SG 1
HETATM 68 N N . TS9 A 1 11 ? 3.231 4.932 -7.175 1.00 9.21 ? 10 TS9 A N 1
HETATM 69 C CA . TS9 A 1 11 ? 2.644 5.261 -5.845 1.00 9.94 ? 10 TS9 A CA 1
HETATM 70 C C . TS9 A 1 11 ? 3.047 6.676 -5.398 1.00 8.20 ? 10 TS9 A C 1
HETATM 71 C CB . TS9 A 1 11 ? 2.939 4.176 -4.798 1.00 10.91 ? 10 TS9 A CB 1
HETATM 72 O OG3 . TS9 A 1 11 ? 4.363 4.010 -4.756 1.00 11.48 ? 10 TS9 A OG3 1
HETATM 73 C CG2 . TS9 A 1 11 ? 2.489 4.637 -3.413 1.00 11.34 ? 10 TS9 A CG2 1
HETATM 74 C CG1 . TS9 A 1 11 ? 2.251 2.864 -5.257 1.00 12.21 ? 10 TS9 A CG1 1
HETATM 75 O OD2 . TS9 A 1 11 ? 0.827 3.035 -5.400 1.00 12.20 ? 10 TS9 A OD2 1
HETATM 76 C CD1 . TS9 A 1 11 ? 2.500 1.710 -4.306 1.00 12.61 ? 10 TS9 A CD1 1
HETATM 77 N N . BB9 A 1 12 ? 4.312 7.001 -5.147 1.00 6.87 ? 11 BB9 A N 1
HETATM 78 C CA . BB9 A 1 12 ? 4.502 8.323 -5.118 1.00 6.56 ? 11 BB9 A CA 1
HETATM 79 C C . BB9 A 1 12 ? 5.814 8.913 -4.817 1.00 5.98 ? 11 BB9 A C 1
HETATM 80 O O . BB9 A 1 12 ? 6.055 10.127 -4.989 1.00 6.29 ? 11 BB9 A O 1
HETATM 81 C CB . BB9 A 1 12 ? 3.403 9.032 -5.430 1.00 6.52 ? 11 BB9 A CB 1
HETATM 82 S SG . BB9 A 1 12 ? 2.070 8.044 -5.706 1.00 6.50 ? 11 BB9 A SG 1
ATOM 83 N N . THR A 1 13 ? 6.872 8.037 -4.580 1.00 5.28 ? 12 THR A N 1
ATOM 84 C CA . THR A 1 13 ? 8.243 8.480 -4.163 1.00 4.99 ? 12 THR A CA 1
ATOM 85 C C . THR A 1 13 ? 9.150 8.418 -5.392 1.00 4.75 ? 12 THR A C 1
ATOM 86 C CB . THR A 1 13 ? 8.735 7.628 -2.997 1.00 5.05 ? 12 THR A CB 1
ATOM 87 O OG1 . THR A 1 13 ? 8.745 6.259 -3.416 1.00 5.11 ? 12 THR A OG1 1
ATOM 88 C CG2 . THR A 1 13 ? 7.869 7.776 -1.759 1.00 5.19 ? 12 THR A CG2 1
HETATM 89 N N . BB9 A 1 14 ? 10.438 8.693 -5.242 1.00 4.68 ? 13 BB9 A N 1
HETATM 90 C CA . BB9 A 1 14 ? 11.025 8.757 -6.413 1.00 4.73 ? 13 BB9 A CA 1
HETATM 91 C C . BB9 A 1 14 ? 12.462 9.086 -6.566 1.00 5.14 ? 13 BB9 A C 1
HETATM 92 C CB . BB9 A 1 14 ? 10.179 8.514 -7.428 1.00 4.65 ? 13 BB9 A CB 1
HETATM 93 S SG . BB9 A 1 14 ? 8.570 8.233 -6.992 1.00 4.36 ? 13 BB9 A SG 1
HETATM 94 N N . MH6 A 1 15 ? 12.677 10.395 -6.191 1.00 5.74 ? 14 MH6 A N 1
HETATM 95 C CA . MH6 A 1 15 ? 13.704 10.877 -5.607 1.00 5.72 ? 14 MH6 A CA 1
HETATM 96 C C . MH6 A 1 15 ? 13.803 12.303 -5.171 1.00 9.27 ? 14 MH6 A C 1
HETATM 97 C CB . MH6 A 1 15 ? 15.011 10.219 -5.309 1.00 5.95 ? 14 MH6 A CB 1
HETATM 98 N N . BB9 A 1 16 ? 14.625 12.665 -4.176 1.00 11.23 ? 15 BB9 A N 1
HETATM 99 C CA . BB9 A 1 16 ? 14.458 13.946 -3.941 1.00 11.87 ? 15 BB9 A CA 1
HETATM 100 C C . BB9 A 1 16 ? 15.449 14.750 -3.201 1.00 12.66 ? 15 BB9 A C 1
HETATM 101 O O . BB9 A 1 16 ? 15.078 15.904 -2.867 1.00 13.48 ? 15 BB9 A O 1
HETATM 102 C CB . BB9 A 1 16 ? 13.347 14.425 -4.459 1.00 11.78 ? 15 BB9 A CB 1
HETATM 103 S SG . BB9 A 1 16 ? 12.434 13.267 -5.281 1.00 11.74 ? 15 BB9 A SG 1
HETATM 104 N N . DHA A 1 17 ? 16.710 14.367 -2.976 1.00 14.44 ? 16 DHA A N 1
HETATM 105 C CA . DHA A 1 17 ? 17.908 14.746 -2.561 1.00 15.77 ? 16 DHA A CA 1
HETATM 106 C CB . DHA A 1 17 ? 17.955 15.671 -1.613 1.00 18.20 ? 16 DHA A CB 1
HETATM 107 C C . DHA A 1 17 ? 19.124 14.169 -3.134 1.00 16.09 ? 16 DHA A C 1
HETATM 108 O O . DHA A 1 17 ? 19.041 13.635 -4.287 1.00 15.91 ? 16 DHA A O 1
HETATM 109 N N . DHA A 1 18 ? 20.286 14.114 -2.382 1.00 15.70 ? 17 DHA A N 1
HETATM 110 C CA . DHA A 1 18 ? 21.522 13.704 -2.713 1.00 15.41 ? 17 DHA A CA 1
HETATM 111 C CB . DHA A 1 18 ? 21.709 12.667 -3.524 1.00 15.59 ? 17 DHA A CB 1
HETATM 112 C C . DHA A 1 18 ? 22.719 14.354 -2.172 1.00 14.77 ? 17 DHA A C 1
HETATM 113 O O . DHA A 1 18 ? 22.595 14.984 -1.101 1.00 14.89 ? 17 DHA A O 1
HETATM 114 N N . NH2 A 1 19 ? 23.856 14.504 -2.745 1.00 14.10 ? 18 NH2 A N 1
HETATM 115 O O . HOH B 2 . ? 5.403 5.113 0.255 0.50 4.25 ? 101 HOH A O 1
HETATM 116 O O . HOH B 2 . ? 5.975 5.285 -2.864 1.00 12.00 ? 102 HOH A O 1
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 QUA 1 0 0 QUA QUA A . n
A 1 2 ILE 2 1 1 ILE ILE A . n
A 1 3 ALA 3 2 2 ALA ALA A . n
A 1 4 DHA 4 3 3 DHA DHA A . n
A 1 5 ALA 5 4 4 ALA ALA A . n
A 1 6 SER 6 5 5 SER SER A . n
A 1 7 BB9 7 6 6 BB9 BB9 A . n
A 1 8 THR 8 7 7 THR THR A . n
A 1 9 DBU 9 8 8 DBU DBU A . n
A 1 10 DCY 10 9 9 DCY DCY A . n
A 1 11 TS9 11 10 10 TS9 TS9 A . n
A 1 12 BB9 12 11 11 BB9 BB9 A . n
A 1 13 THR 13 12 12 THR THR A . n
A 1 14 BB9 14 13 13 BB9 BB9 A . n
A 1 15 MH6 15 14 14 MH6 MH6 A . n
A 1 16 BB9 16 15 15 BB9 BB9 A . n
A 1 17 DHA 17 16 16 DHA DHA A . n
A 1 18 DHA 18 17 17 DHA DHA A . n
A 1 19 NH2 19 18 18 NH2 NH2 A . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 HOH 1 101 1 HOH HOH A .
B 2 HOH 2 102 2 HOH HOH A .
#
_pdbx_molecule_features.prd_id PRD_000223
_pdbx_molecule_features.name THIOSTREPTON
_pdbx_molecule_features.type Thiopeptide
_pdbx_molecule_features.class Antibiotic
_pdbx_molecule_features.details
;Thiostrepton is a hetrocyclic thiopeptide belonging to the
thiocillin family, consisting of four thiazole, one thiozoline and one
piperideine rings. A modified quinoline linked to main-chain residue 1
and side-chain of residue 12. Post translational maturation of
thiazole and oxazole containing antibiotics involves the enzymic
condensation of a Cys or Ser with the alpha-carbonyl of the preceding
amino acid to form a thioether or ether bond, then dehydration to form
a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline
ring are dehydrogenated to form thiazole or oxazole rings. the
pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair
usually separated by 7 or 8 residues along the peptide chain. The Ser
residues are dehydrated to didehydroalanines, then bonded between
their beta carbons. The alpha carbonyl of the Cys condenses with alpha
carbon of the first Ser to form a pyridinyl ring. The ring may be
mutiply dehydrogenated to form a pyridine ring with loss of the amino
nitrogen of the first Ser. The amidation of Ser-17 probably does not
occur by the same mechanism, oxidative cleavage of glycine, as in
eukaryotes.
;
#
_pdbx_molecule.instance_id 1
_pdbx_molecule.prd_id PRD_000223
_pdbx_molecule.asym_id A
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details monomeric
_pdbx_struct_assembly.oligomeric_count 1
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B
#
loop_
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
1 'ABSA (A^2)' 400 ?
1 MORE 1 ?
1 'SSA (A^2)' 1690 ?
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2018-11-21
2 'Structure model' 1 1 2019-01-02
3 'Structure model' 1 2 2019-02-06
4 'Structure model' 2 0 2019-11-27
5 'Structure model' 2 1 2023-10-11
6 'Structure model' 2 2 2023-11-15
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Data collection'
2 2 'Structure model' 'Database references'
3 2 'Structure model' 'Derived calculations'
4 3 'Structure model' 'Data collection'
5 3 'Structure model' 'Database references'
6 4 'Structure model' 'Author supporting evidence'
7 4 'Structure model' 'Polymer sequence'
8 5 'Structure model' 'Data collection'
9 5 'Structure model' 'Database references'
10 5 'Structure model' 'Derived calculations'
11 5 'Structure model' 'Refinement description'
12 6 'Structure model' 'Data collection'
13 6 'Structure model' 'Derived calculations'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 2 'Structure model' citation
2 2 'Structure model' citation_author
3 2 'Structure model' diffrn_radiation_wavelength
4 2 'Structure model' diffrn_source
5 2 'Structure model' struct_site
6 2 'Structure model' struct_site_gen
7 3 'Structure model' struct_ref
8 4 'Structure model' entity_poly
9 4 'Structure model' pdbx_audit_support
10 5 'Structure model' chem_comp_atom
11 5 'Structure model' chem_comp_bond
12 5 'Structure model' database_2
13 5 'Structure model' em_3d_fitting_list
14 5 'Structure model' pdbx_initial_refinement_model
15 5 'Structure model' struct_conn
16 6 'Structure model' chem_comp_atom
17 6 'Structure model' chem_comp_bond
18 6 'Structure model' struct_conn
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 2 'Structure model' '_citation.journal_abbrev'
2 2 'Structure model' '_citation.journal_id_ISSN'
3 2 'Structure model' '_citation.journal_volume'
4 2 'Structure model' '_citation.page_first'
5 2 'Structure model' '_citation.page_last'
6 2 'Structure model' '_citation.pdbx_database_id_PubMed'
7 2 'Structure model' '_citation.title'
8 2 'Structure model' '_citation_author.identifier_ORCID'
9 2 'Structure model' '_citation_author.name'
10 3 'Structure model' '_struct_ref.db_name'
11 3 'Structure model' '_struct_ref.pdbx_db_accession'
12 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can'
13 4 'Structure model' '_pdbx_audit_support.funding_organization'
14 5 'Structure model' '_database_2.pdbx_DOI'
15 5 'Structure model' '_database_2.pdbx_database_accession'
16 5 'Structure model' '_em_3d_fitting_list.accession_code'
17 5 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id'
18 5 'Structure model' '_em_3d_fitting_list.source_name'
19 5 'Structure model' '_em_3d_fitting_list.type'
20 5 'Structure model' '_struct_conn.pdbx_dist_value'
21 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'
22 5 'Structure model' '_struct_conn.ptnr1_label_atom_id'
23 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id'
24 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id'
25 5 'Structure model' '_struct_conn.ptnr2_label_atom_id'
26 5 'Structure model' '_struct_conn.ptnr2_label_comp_id'
27 5 'Structure model' '_struct_conn.ptnr2_label_seq_id'
28 6 'Structure model' '_chem_comp_atom.atom_id'
29 6 'Structure model' '_chem_comp_bond.atom_id_2'
30 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag'
#
loop_
_software.citation_id
_software.classification
_software.compiler_name
_software.compiler_version
_software.contact_author
_software.contact_author_email
_software.date
_software.description
_software.dependencies
_software.hardware
_software.language
_software.location
_software.mods
_software.name
_software.os
_software.os_version
_software.type
_software.version
_software.pdbx_ordinal
? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0238 1
? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? MOSFLM ? ? ? 7.2.2 2
? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? 0.7.3 3
? phasing ? ? ? ? ? ? ? ? ? ? ? MOLREP ? ? ? 11.6.04 4
#
_pdbx_entry_details.entry_id 6MXF
_pdbx_entry_details.compound_details
;THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES
CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A
NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO
ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING
THIAZOLES, THIAZOLINES AND OXAZOLES.
HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)
;
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
_pdbx_entry_details.has_ligand_of_interest ?
#
_em_3d_fitting.entry_id 6MXF
_em_3d_fitting.id 1
_em_3d_fitting.details ?
_em_3d_fitting.overall_b_value 2.6
_em_3d_fitting.ref_protocol OTHER
_em_3d_fitting.ref_space RECIPROCAL
_em_3d_fitting.target_criteria ?
_em_3d_fitting.method ?
#
_em_3d_fitting_list.3d_fitting_id 1
_em_3d_fitting_list.id 1
_em_3d_fitting_list.details ?
_em_3d_fitting_list.pdb_chain_id A
_em_3d_fitting_list.pdb_chain_residue_range 0-18
_em_3d_fitting_list.pdb_entry_id 1E9W
_em_3d_fitting_list.initial_refinement_model_id 1
_em_3d_fitting_list.chain_id ?
_em_3d_fitting_list.chain_residue_range ?
_em_3d_fitting_list.source_name PDB
_em_3d_fitting_list.type 'experimental model'
_em_3d_fitting_list.accession_code 1E9W
#
_em_3d_reconstruction.entry_id 6MXF
_em_3d_reconstruction.id 1
_em_3d_reconstruction.algorithm ?
_em_3d_reconstruction.details ?
_em_3d_reconstruction.refinement_type ?
_em_3d_reconstruction.image_processing_id 1
_em_3d_reconstruction.num_class_averages ?
_em_3d_reconstruction.num_particles ?
_em_3d_reconstruction.resolution 1.91
_em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES'
_em_3d_reconstruction.symmetry_type '3D CRYSTAL'
_em_3d_reconstruction.method ?
_em_3d_reconstruction.nominal_pixel_size ?
_em_3d_reconstruction.actual_pixel_size ?
_em_3d_reconstruction.magnification_calibration ?
#
_em_buffer.id 1
_em_buffer.details Powder
_em_buffer.pH 7
_em_buffer.specimen_id 1
_em_buffer.name ?
#
_em_entity_assembly.id 1
_em_entity_assembly.parent_id 0
_em_entity_assembly.details ?
_em_entity_assembly.name Thiostrepton
_em_entity_assembly.source NATURAL
_em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT'
_em_entity_assembly.entity_id_list 1
_em_entity_assembly.synonym ?
_em_entity_assembly.oligomeric_details ?
#
_em_image_scans.entry_id 6MXF
_em_image_scans.id 1
_em_image_scans.dimension_height 2048
_em_image_scans.dimension_width 2048
_em_image_scans.frames_per_image ?
_em_image_scans.image_recording_id 1
_em_image_scans.sampling_size 28
_em_image_scans.scanner_model ?
_em_image_scans.used_frames_per_image ?
_em_image_scans.citation_id ?
_em_image_scans.number_digital_images ?
_em_image_scans.od_range ?
_em_image_scans.quant_bit_size ?
_em_image_scans.details ?
#
_em_imaging.id 1
_em_imaging.entry_id 6MXF
_em_imaging.accelerating_voltage 200
_em_imaging.alignment_procedure ?
_em_imaging.c2_aperture_diameter ?
_em_imaging.calibrated_defocus_max ?
_em_imaging.calibrated_defocus_min ?
_em_imaging.calibrated_magnification ?
_em_imaging.cryogen NITROGEN
_em_imaging.details ?
_em_imaging.electron_source 'FIELD EMISSION GUN'
_em_imaging.illumination_mode 'FLOOD BEAM'
_em_imaging.microscope_model 'FEI TALOS ARCTICA'
_em_imaging.mode DIFFRACTION
_em_imaging.nominal_cs ?
_em_imaging.nominal_defocus_max ?
_em_imaging.nominal_defocus_min ?
_em_imaging.nominal_magnification ?
_em_imaging.recording_temperature_maximum ?
_em_imaging.recording_temperature_minimum ?
_em_imaging.residual_tilt ?
_em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER'
_em_imaging.specimen_id 1
_em_imaging.citation_id ?
_em_imaging.date ?
_em_imaging.temperature ?
_em_imaging.tilt_angle_min ?
_em_imaging.tilt_angle_max ?
_em_imaging.astigmatism ?
_em_imaging.detector_distance ?
_em_imaging.electron_beam_tilt_params ?
_em_imaging.specimen_holder_type ?
#
_em_sample_support.id 1
_em_sample_support.specimen_id 1
_em_sample_support.details ?
_em_sample_support.grid_material COPPER
_em_sample_support.grid_mesh_size 300
_em_sample_support.grid_type 'Quantifoil R2/2'
_em_sample_support.method ?
_em_sample_support.film_material ?
#
_em_vitrification.id 1
_em_vitrification.specimen_id 1
_em_vitrification.chamber_temperature 298
_em_vitrification.cryogen_name NITROGEN
_em_vitrification.details Hand-plunged
_em_vitrification.humidity 100
_em_vitrification.instrument ?
_em_vitrification.entry_id 6MXF
_em_vitrification.citation_id ?
_em_vitrification.method ?
_em_vitrification.temp ?
_em_vitrification.time_resolved_state ?
#
_em_experiment.entry_id 6MXF
_em_experiment.id 1
_em_experiment.aggregation_state '3D ARRAY'
_em_experiment.reconstruction_method CRYSTALLOGRAPHY
_em_experiment.entity_assembly_id 1
#
_pdbx_validate_close_contact.id 1
_pdbx_validate_close_contact.PDB_model_num 1
_pdbx_validate_close_contact.auth_atom_id_1 O12
_pdbx_validate_close_contact.auth_asym_id_1 A
_pdbx_validate_close_contact.auth_comp_id_1 QUA
_pdbx_validate_close_contact.auth_seq_id_1 0
_pdbx_validate_close_contact.PDB_ins_code_1 ?
_pdbx_validate_close_contact.label_alt_id_1 ?
_pdbx_validate_close_contact.auth_atom_id_2 OG1
_pdbx_validate_close_contact.auth_asym_id_2 A
_pdbx_validate_close_contact.auth_comp_id_2 THR
_pdbx_validate_close_contact.auth_seq_id_2 12
_pdbx_validate_close_contact.PDB_ins_code_2 ?
_pdbx_validate_close_contact.label_alt_id_2 ?
_pdbx_validate_close_contact.dist 2.13
#
_pdbx_validate_rmsd_angle.id 1
_pdbx_validate_rmsd_angle.PDB_model_num 1
_pdbx_validate_rmsd_angle.auth_atom_id_1 C
_pdbx_validate_rmsd_angle.auth_asym_id_1 A
_pdbx_validate_rmsd_angle.auth_comp_id_1 BB9
_pdbx_validate_rmsd_angle.auth_seq_id_1 15
_pdbx_validate_rmsd_angle.PDB_ins_code_1 ?
_pdbx_validate_rmsd_angle.label_alt_id_1 ?
_pdbx_validate_rmsd_angle.auth_atom_id_2 N
_pdbx_validate_rmsd_angle.auth_asym_id_2 A
_pdbx_validate_rmsd_angle.auth_comp_id_2 DHA
_pdbx_validate_rmsd_angle.auth_seq_id_2 16
_pdbx_validate_rmsd_angle.PDB_ins_code_2 ?
_pdbx_validate_rmsd_angle.label_alt_id_2 ?
_pdbx_validate_rmsd_angle.auth_atom_id_3 CA
_pdbx_validate_rmsd_angle.auth_asym_id_3 A
_pdbx_validate_rmsd_angle.auth_comp_id_3 DHA
_pdbx_validate_rmsd_angle.auth_seq_id_3 16
_pdbx_validate_rmsd_angle.PDB_ins_code_3 ?
_pdbx_validate_rmsd_angle.label_alt_id_3 ?
_pdbx_validate_rmsd_angle.angle_value 145.55
_pdbx_validate_rmsd_angle.angle_target_value 121.70
_pdbx_validate_rmsd_angle.angle_deviation 23.85
_pdbx_validate_rmsd_angle.angle_standard_deviation 2.50
_pdbx_validate_rmsd_angle.linker_flag Y
#
loop_
_pdbx_validate_torsion.id
_pdbx_validate_torsion.PDB_model_num
_pdbx_validate_torsion.auth_comp_id
_pdbx_validate_torsion.auth_asym_id
_pdbx_validate_torsion.auth_seq_id
_pdbx_validate_torsion.PDB_ins_code
_pdbx_validate_torsion.label_alt_id
_pdbx_validate_torsion.phi
_pdbx_validate_torsion.psi
1 1 SER A 5 ? ? 63.70 77.93
2 1 DCY A 9 ? ? -135.15 -2.00
#
_pdbx_validate_peptide_omega.id 1
_pdbx_validate_peptide_omega.PDB_model_num 1
_pdbx_validate_peptide_omega.auth_comp_id_1 BB9
_pdbx_validate_peptide_omega.auth_asym_id_1 A
_pdbx_validate_peptide_omega.auth_seq_id_1 13
_pdbx_validate_peptide_omega.PDB_ins_code_1 ?
_pdbx_validate_peptide_omega.label_alt_id_1 ?
_pdbx_validate_peptide_omega.auth_comp_id_2 MH6
_pdbx_validate_peptide_omega.auth_asym_id_2 A
_pdbx_validate_peptide_omega.auth_seq_id_2 14
_pdbx_validate_peptide_omega.PDB_ins_code_2 ?
_pdbx_validate_peptide_omega.label_alt_id_2 ?
_pdbx_validate_peptide_omega.omega 145.15
#
_pdbx_validate_main_chain_plane.id 1
_pdbx_validate_main_chain_plane.PDB_model_num 1
_pdbx_validate_main_chain_plane.auth_comp_id BB9
_pdbx_validate_main_chain_plane.auth_asym_id A
_pdbx_validate_main_chain_plane.auth_seq_id 6
_pdbx_validate_main_chain_plane.PDB_ins_code ?
_pdbx_validate_main_chain_plane.label_alt_id ?
_pdbx_validate_main_chain_plane.improper_torsion_angle 14.10
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
ALA N N N N 1
ALA CA C N S 2
ALA C C N N 3
ALA O O N N 4
ALA CB C N N 5
ALA OXT O N N 6
ALA H H N N 7
ALA H2 H N N 8
ALA HA H N N 9
ALA HB1 H N N 10
ALA HB2 H N N 11
ALA HB3 H N N 12
ALA HXT H N N 13
BB9 N N N N 14
BB9 CA C N N 15
BB9 C C N N 16
BB9 O O N N 17
BB9 CB C N N 18
BB9 SG S N N 19
BB9 OXT O N N 20
BB9 H H N N 21
BB9 H2 H N N 22
BB9 HB H N N 23
BB9 HXT H N N 24
BB9 HG H N N 25
DBU N N N N 26
DBU CA C N N 27
DBU CB C N N 28
DBU CG C N N 29
DBU C C N N 30
DBU O O N N 31
DBU OXT O N N 32
DBU H H N N 33
DBU H2 H N N 34
DBU HB H N N 35
DBU HG1 H N N 36
DBU HG2 H N N 37
DBU HG3 H N N 38
DBU HXT H N N 39
DCY N N N N 40
DCY CA C N S 41
DCY C C N N 42
DCY O O N N 43
DCY CB C N N 44
DCY SG S N N 45
DCY OXT O N N 46
DCY H H N N 47
DCY H2 H N N 48
DCY HA H N N 49
DCY HB2 H N N 50
DCY HB3 H N N 51
DCY HG H N N 52
DCY HXT H N N 53
DHA N N N N 54
DHA CA C N N 55
DHA CB C N N 56
DHA C C N N 57
DHA O O N N 58
DHA OXT O N N 59
DHA H H N N 60
DHA H2 H N N 61
DHA HB1 H N N 62
DHA HB2 H N N 63
DHA HXT H N N 64
HOH O O N N 65
HOH H1 H N N 66
HOH H2 H N N 67
ILE N N N N 68
ILE CA C N S 69
ILE C C N N 70
ILE O O N N 71
ILE CB C N S 72
ILE CG1 C N N 73
ILE CG2 C N N 74
ILE CD1 C N N 75
ILE OXT O N N 76
ILE H H N N 77
ILE H2 H N N 78
ILE HA H N N 79
ILE HB H N N 80
ILE HG12 H N N 81
ILE HG13 H N N 82
ILE HG21 H N N 83
ILE HG22 H N N 84
ILE HG23 H N N 85
ILE HD11 H N N 86
ILE HD12 H N N 87
ILE HD13 H N N 88
ILE HXT H N N 89
MH6 N N N N 90
MH6 CA C N N 91
MH6 C C N N 92
MH6 CB C N N 93
MH6 OG O N N 94
MH6 O O N N 95
MH6 OXT O N N 96
MH6 H H N N 97
MH6 HB2 H N N 98
MH6 HB3 H N N 99
MH6 HXT H N N 100
MH6 HG H N N 101
NH2 N N N N 102
NH2 HN1 H N N 103
NH2 HN2 H N N 104
QUA O12 O N N 105
QUA C11 C N N 106
QUA C2 C Y N 107
QUA N1 N Y N 108
QUA C3 C Y N 109
QUA C9 C Y N 110
QUA C4 C Y N 111
QUA C8 C N S 112
QUA C10 C Y N 113
QUA O16 O N N 114
QUA C7 C N N 115
QUA C13 C N S 116
QUA O15 O N N 117
QUA C5 C N N 118
QUA C14 C N N 119
QUA C6 C N N 120
QUA "O1'" O N N 121
QUA HC3 H N N 122
QUA HC8 H N N 123
QUA H16 H N N 124
QUA HC71 H N N 125
QUA HC72 H N N 126
QUA H13 H N N 127
QUA H15 H N N 128
QUA HC5 H N N 129
QUA H141 H N N 130
QUA H142 H N N 131
QUA H143 H N N 132
QUA HC6 H N N 133
QUA "H1'" H N N 134
SER N N N N 135
SER CA C N S 136
SER C C N N 137
SER O O N N 138
SER CB C N N 139
SER OG O N N 140
SER OXT O N N 141
SER H H N N 142
SER H2 H N N 143
SER HA H N N 144
SER HB2 H N N 145
SER HB3 H N N 146
SER HG H N N 147
SER HXT H N N 148
THR N N N N 149
THR CA C N S 150
THR C C N N 151
THR O O N N 152
THR CB C N R 153
THR OG1 O N N 154
THR CG2 C N N 155
THR OXT O N N 156
THR H H N N 157
THR H2 H N N 158
THR HA H N N 159
THR HB H N N 160
THR HG1 H N N 161
THR HG21 H N N 162
THR HG22 H N N 163
THR HG23 H N N 164
THR HXT H N N 165
TS9 N N N N 166
TS9 CA C N S 167
TS9 C C N N 168
TS9 CB C N S 169
TS9 OG3 O N N 170
TS9 CG2 C N N 171
TS9 CG1 C N R 172
TS9 OD2 O N N 173
TS9 CD1 C N N 174
TS9 OXT O N N 175
TS9 O O N N 176
TS9 H H N N 177
TS9 H2 H N N 178
TS9 HA H N N 179
TS9 HXT H N N 180
TS9 HG3 H N N 181
TS9 HG21 H N N 182
TS9 HG22 H N N 183
TS9 HG23 H N N 184
TS9 HG1 H N N 185
TS9 HD2 H N N 186
TS9 HD11 H N N 187
TS9 HD12 H N N 188
TS9 HD13 H N N 189
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
ALA N CA sing N N 1
ALA N H sing N N 2
ALA N H2 sing N N 3
ALA CA C sing N N 4
ALA CA CB sing N N 5
ALA CA HA sing N N 6
ALA C O doub N N 7
ALA C OXT sing N N 8
ALA CB HB1 sing N N 9
ALA CB HB2 sing N N 10
ALA CB HB3 sing N N 11
ALA OXT HXT sing N N 12
BB9 N CA sing N N 13
BB9 CA C sing N N 14
BB9 CA CB doub N N 15
BB9 C O doub N N 16
BB9 C OXT sing N Z 17
BB9 CB SG sing N N 18
BB9 N H sing N N 19
BB9 N H2 sing N N 20
BB9 CB HB sing N N 21
BB9 OXT HXT sing N N 22
BB9 SG HG sing N N 23
DBU N CA sing N N 24
DBU N H sing N N 25
DBU N H2 sing N N 26
DBU CA CB doub N Z 27
DBU CA C sing N N 28
DBU CB CG sing N N 29
DBU CB HB sing N N 30
DBU CG HG1 sing N N 31
DBU CG HG2 sing N N 32
DBU CG HG3 sing N N 33
DBU C O doub N N 34
DBU C OXT sing N N 35
DBU OXT HXT sing N N 36
DCY N CA sing N N 37
DCY N H sing N N 38
DCY N H2 sing N N 39
DCY CA C sing N N 40
DCY CA CB sing N N 41
DCY CA HA sing N N 42
DCY C O doub N N 43
DCY C OXT sing N N 44
DCY CB SG sing N N 45
DCY CB HB2 sing N N 46
DCY CB HB3 sing N N 47
DCY SG HG sing N N 48
DCY OXT HXT sing N N 49
DHA N CA sing N N 50
DHA N H sing N N 51
DHA N H2 sing N N 52
DHA CA CB doub N N 53
DHA CA C sing N N 54
DHA CB HB1 sing N N 55
DHA CB HB2 sing N N 56
DHA C O doub N N 57
DHA C OXT sing N N 58
DHA OXT HXT sing N N 59
HOH O H1 sing N N 60
HOH O H2 sing N N 61
ILE N CA sing N N 62
ILE N H sing N N 63
ILE N H2 sing N N 64
ILE CA C sing N N 65
ILE CA CB sing N N 66
ILE CA HA sing N N 67
ILE C O doub N N 68
ILE C OXT sing N N 69
ILE CB CG1 sing N N 70
ILE CB CG2 sing N N 71
ILE CB HB sing N N 72
ILE CG1 CD1 sing N N 73
ILE CG1 HG12 sing N N 74
ILE CG1 HG13 sing N N 75
ILE CG2 HG21 sing N N 76
ILE CG2 HG22 sing N N 77
ILE CG2 HG23 sing N N 78
ILE CD1 HD11 sing N N 79
ILE CD1 HD12 sing N N 80
ILE CD1 HD13 sing N N 81
ILE OXT HXT sing N N 82
MH6 N CA doub N N 83
MH6 CA C sing N N 84
MH6 CA CB sing N N 85
MH6 C O doub N N 86
MH6 C OXT sing N N 87
MH6 CB OG sing N N 88
MH6 N H sing N N 89
MH6 CB HB2 sing N N 90
MH6 CB HB3 sing N N 91
MH6 OXT HXT sing N N 92
MH6 OG HG sing N N 93
NH2 N HN1 sing N N 94
NH2 N HN2 sing N N 95
QUA O12 C11 doub N N 96
QUA C11 C2 sing N N 97
QUA C11 "O1'" sing N N 98
QUA C2 N1 doub Y N 99
QUA C2 C3 sing Y N 100
QUA N1 C9 sing Y N 101
QUA C3 C4 doub Y N 102
QUA C3 HC3 sing N N 103
QUA C9 C8 sing N N 104
QUA C9 C10 doub Y N 105
QUA C4 C10 sing Y N 106
QUA C4 C13 sing N N 107
QUA C8 O16 sing N N 108
QUA C8 C7 sing N N 109
QUA C8 HC8 sing N N 110
QUA C10 C5 sing N N 111
QUA O16 H16 sing N N 112
QUA C7 C6 sing N N 113
QUA C7 HC71 sing N N 114
QUA C7 HC72 sing N N 115
QUA C13 O15 sing N N 116
QUA C13 C14 sing N N 117
QUA C13 H13 sing N N 118
QUA O15 H15 sing N N 119
QUA C5 C6 doub N N 120
QUA C5 HC5 sing N N 121
QUA C14 H141 sing N N 122
QUA C14 H142 sing N N 123
QUA C14 H143 sing N N 124
QUA C6 HC6 sing N N 125
QUA "O1'" "H1'" sing N N 126
SER N CA sing N N 127
SER N H sing N N 128
SER N H2 sing N N 129
SER CA C sing N N 130
SER CA CB sing N N 131
SER CA HA sing N N 132
SER C O doub N N 133
SER C OXT sing N N 134
SER CB OG sing N N 135
SER CB HB2 sing N N 136
SER CB HB3 sing N N 137
SER OG HG sing N N 138
SER OXT HXT sing N N 139
THR N CA sing N N 140
THR N H sing N N 141
THR N H2 sing N N 142
THR CA C sing N N 143
THR CA CB sing N N 144
THR CA HA sing N N 145
THR C O doub N N 146
THR C OXT sing N N 147
THR CB OG1 sing N N 148
THR CB CG2 sing N N 149
THR CB HB sing N N 150
THR OG1 HG1 sing N N 151
THR CG2 HG21 sing N N 152
THR CG2 HG22 sing N N 153
THR CG2 HG23 sing N N 154
THR OXT HXT sing N N 155
TS9 N CA sing N N 156
TS9 CA C sing N N 157
TS9 CA CB sing N N 158
TS9 C OXT sing N N 159
TS9 C O doub N N 160
TS9 CB OG3 sing N N 161
TS9 CB CG2 sing N N 162
TS9 CB CG1 sing N N 163
TS9 CG1 OD2 sing N N 164
TS9 CG1 CD1 sing N N 165
TS9 N H sing N N 166
TS9 N H2 sing N N 167
TS9 CA HA sing N N 168
TS9 OXT HXT sing N N 169
TS9 OG3 HG3 sing N N 170
TS9 CG2 HG21 sing N N 171
TS9 CG2 HG22 sing N N 172
TS9 CG2 HG23 sing N N 173
TS9 CG1 HG1 sing N N 174
TS9 OD2 HD2 sing N N 175
TS9 CD1 HD11 sing N N 176
TS9 CD1 HD12 sing N N 177
TS9 CD1 HD13 sing N N 178
#
_em_3d_crystal_entity.id 1
_em_3d_crystal_entity.image_processing_id 1
_em_3d_crystal_entity.angle_alpha 90
_em_3d_crystal_entity.angle_beta 90
_em_3d_crystal_entity.angle_gamma 90
_em_3d_crystal_entity.length_a 26.219
_em_3d_crystal_entity.length_b 26.219
_em_3d_crystal_entity.length_c 27.534
_em_3d_crystal_entity.space_group_name 'P 43 21 2'
_em_3d_crystal_entity.space_group_num 96
#
_em_crystal_formation.id 1
_em_crystal_formation.specimen_id 1
_em_crystal_formation.atmosphere ?
_em_crystal_formation.details Powder
_em_crystal_formation.instrument ?
_em_crystal_formation.lipid_mixture ?
_em_crystal_formation.lipid_protein_ratio ?
_em_crystal_formation.temperature ?
_em_crystal_formation.time ?
_em_crystal_formation.time_unit ?
#
_em_ctf_correction.id 1
_em_ctf_correction.em_image_processing_id 1
_em_ctf_correction.type NONE
_em_ctf_correction.details ?
#
_em_diffraction.id 1
_em_diffraction.camera_length 960
_em_diffraction.imaging_id 1
_em_diffraction.tilt_angle_list ?
#
_em_diffraction_shell.id 1
_em_diffraction_shell.em_diffraction_stats_id 1
_em_diffraction_shell.fourier_space_coverage 40.3
_em_diffraction_shell.high_resolution 1.91
_em_diffraction_shell.low_resolution 2.13
_em_diffraction_shell.multiplicity 4.9
_em_diffraction_shell.num_structure_factors 92
_em_diffraction_shell.phase_residual 29.19
#
_em_diffraction_stats.id 1
_em_diffraction_stats.details ?
_em_diffraction_stats.image_processing_id 1
_em_diffraction_stats.fourier_space_coverage 78.6
_em_diffraction_stats.high_resolution 1.91
_em_diffraction_stats.num_intensities_measured 5578
_em_diffraction_stats.num_structure_factors 686
_em_diffraction_stats.overall_phase_error 26.93
_em_diffraction_stats.overall_phase_residual 26.93
_em_diffraction_stats.phase_error_rejection_criteria 0
_em_diffraction_stats.r_merge 0.236
_em_diffraction_stats.r_sym 0.236
#
_em_entity_assembly_molwt.entity_assembly_id 1
_em_entity_assembly_molwt.id 1
_em_entity_assembly_molwt.experimental_flag NO
_em_entity_assembly_molwt.units MEGADALTONS
_em_entity_assembly_molwt.value .001619538000
#
_em_entity_assembly_naturalsource.id 2
_em_entity_assembly_naturalsource.entity_assembly_id 1
_em_entity_assembly_naturalsource.cell ?
_em_entity_assembly_naturalsource.cellular_location ?
_em_entity_assembly_naturalsource.ncbi_tax_id 146537
_em_entity_assembly_naturalsource.organ ?
_em_entity_assembly_naturalsource.organelle ?
_em_entity_assembly_naturalsource.organism 'Streptomyces azureus'
_em_entity_assembly_naturalsource.strain ?
_em_entity_assembly_naturalsource.tissue ?
#
_em_image_processing.id 1
_em_image_processing.image_recording_id 1
_em_image_processing.details 'FEI Ceta'
#
_em_image_recording.id 1
_em_image_recording.imaging_id 1
_em_image_recording.avg_electron_dose_per_image 0.09
_em_image_recording.average_exposure_time 2.21
_em_image_recording.details 'FEI CetaD'
_em_image_recording.detector_mode ?
_em_image_recording.film_or_detector_model 'FEI CETA (4k x 4k)'
_em_image_recording.num_diffraction_images 214
_em_image_recording.num_grids_imaged 1
_em_image_recording.num_real_images ?
#
_em_imaging_optics.id 1
_em_imaging_optics.imaging_id 1
_em_imaging_optics.chr_aberration_corrector ?
_em_imaging_optics.energyfilter_lower ?
_em_imaging_optics.energyfilter_name ?
_em_imaging_optics.energyfilter_upper ?
_em_imaging_optics.energyfilter_slit_width ?
_em_imaging_optics.phase_plate ?
_em_imaging_optics.sph_aberration_corrector ?
#
loop_
_em_software.id
_em_software.category
_em_software.details
_em_software.name
_em_software.version
_em_software.image_processing_id
_em_software.fitting_id
_em_software.imaging_id
1 'IMAGE ACQUISITION' ? ? ? ? ? 1
2 MASKING ? ? ? ? ? ?
3 'CTF CORRECTION' ? ? ? 1 ? ?
4 'LAYERLINE INDEXING' ? ? ? ? ? ?
5 'DIFFRACTION INDEXING' ? ? ? ? ? ?
6 'MODEL FITTING' ? MOLREP 11.6.04 ? 1 ?
7 OTHER ? ? ? ? ? ?
8 'MOLECULAR REPLACEMENT' ? MOLREP 11.6.04 1 ? ?
9 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ?
10 'SYMMETRY DETERMINATION' ? POINTLESS 1.11.14 1 ? ?
11 'CRYSTALLOGRAPHY MERGING' ? AIMLESS 0.7.3 1 ? ?
12 RECONSTRUCTION ? ? ? 1 ? ?
13 'MODEL REFINEMENT' ? REFMAC 5.8.0232 ? 1 ?
#
_em_specimen.id 1
_em_specimen.experiment_id 1
_em_specimen.concentration ?
_em_specimen.details Powder
_em_specimen.embedding_applied NO
_em_specimen.shadowing_applied NO
_em_specimen.staining_applied NO
_em_specimen.vitrification_applied YES
#
loop_
_pdbx_audit_support.funding_organization
_pdbx_audit_support.country
_pdbx_audit_support.grant_number
_pdbx_audit_support.ordinal
'National Science Foundation (NSF, United States)' 'United States' DGE-1650604 1
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' R01GM080269 2
'Department of Energy (DOE, United States)' 'United States' DE-FC02-02ER63421 3
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' R35GM128867 4
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' R35GM128936 5
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name water
_pdbx_entity_nonpoly.comp_id HOH
#
_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list ?
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 1E9W
_pdbx_initial_refinement_model.details ?
#
_pdbx_struct_assembly_auth_evidence.id 1
_pdbx_struct_assembly_auth_evidence.assembly_id 1
_pdbx_struct_assembly_auth_evidence.experimental_support none
_pdbx_struct_assembly_auth_evidence.details ?
#