data_8YG2
#
_entry.id 8YG2
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.398
_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 8YG2 pdb_00008yg2 10.2210/pdb8yg2/pdb
WWPDB D_1300045581 ? ?
#
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 2024-05-08
2 'Structure model' 1 1 2024-11-20
#
_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 ?
#
_pdbx_audit_revision_group.ordinal 1
_pdbx_audit_revision_group.revision_ordinal 2
_pdbx_audit_revision_group.data_content_type 'Structure model'
_pdbx_audit_revision_group.group 'Structure summary'
#
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' pdbx_entry_details
2 2 'Structure model' pdbx_modification_feature
#
_pdbx_audit_revision_item.ordinal 1
_pdbx_audit_revision_item.revision_ordinal 2
_pdbx_audit_revision_item.data_content_type 'Structure model'
_pdbx_audit_revision_item.item '_pdbx_entry_details.has_protein_modification'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 8YG2
_pdbx_database_status.recvd_initial_deposition_date 2024-02-26
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site PDBJ
_pdbx_database_status.process_site PDBJ
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
#
_pdbx_contact_author.id 2
_pdbx_contact_author.email ysohma@wakayama-med.ac.jp
_pdbx_contact_author.name_first Youhei
_pdbx_contact_author.name_last Sohma
_pdbx_contact_author.name_mi ?
_pdbx_contact_author.role 'principal investigator/group leader'
_pdbx_contact_author.identifier_ORCID 0000-0002-1154-3903
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Sawazaki, T.' 1 0000-0001-5650-998X
'Sasaki, D.' 2 0000-0002-2224-1900
'Sohma, Y.' 3 0000-0002-1154-3903
#
_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 Proc.Natl.Acad.Sci.USA
_citation.journal_id_ASTM PNASA6
_citation.journal_id_CSD 0040
_citation.journal_id_ISSN 1091-6490
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume 121
_citation.language ?
_citation.page_first e2314704121
_citation.page_last e2314704121
_citation.title 'Catalysis driven by an amyloid-substrate complex.'
_citation.year 2024
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1073/pnas.2314704121
_citation.pdbx_database_id_PubMed 38691589
_citation.pdbx_database_id_patent ?
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Sawazaki, T.' 1 0000-0001-5650-998X
primary 'Sasaki, D.' 2 0000-0002-2224-1900
primary 'Sohma, Y.' 3 0000-0002-1154-3903
#
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 'Amyloidogenic peptide from Islet Amyloid Polypeptide' 715.862 1 ? ? ? ?
2 non-polymer syn 'FORMIC ACID' 46.025 1 ? ? ? ?
#
_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 '(PIV)NFGAIL(NH2)'
_entity_poly.pdbx_seq_one_letter_code_can XNFGAILX
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name 'FORMIC ACID'
_pdbx_entity_nonpoly.comp_id FMT
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 PIV n
1 2 ASN n
1 3 PHE n
1 4 GLY n
1 5 ALA n
1 6 ILE n
1 7 LEU n
1 8 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 8
_pdbx_entity_src_syn.organism_scientific 'Homo sapiens'
_pdbx_entity_src_syn.organism_common_name human
_pdbx_entity_src_syn.ncbi_taxonomy_id 9606
_pdbx_entity_src_syn.details ?
#
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
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
FMT non-polymer . 'FORMIC ACID' ? 'C H2 O2' 46.025
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173
NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
PIV 'L-peptide linking' . 'PIVALIC ACID' ? 'C5 H10 O2' 102.132
#
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 PIV 1 0 0 PIV PIV A . n
A 1 2 ASN 2 1 1 ASN ASN A . n
A 1 3 PHE 3 2 2 PHE PHE A . n
A 1 4 GLY 4 3 3 GLY GLY A . n
A 1 5 ALA 5 4 4 ALA ALA A . n
A 1 6 ILE 6 5 5 ILE ILE A . n
A 1 7 LEU 7 6 6 LEU LEU A . n
A 1 8 NH2 8 7 7 NH2 NH2 A . n
#
_pdbx_nonpoly_scheme.asym_id B
_pdbx_nonpoly_scheme.entity_id 2
_pdbx_nonpoly_scheme.mon_id FMT
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.pdb_seq_num 101
_pdbx_nonpoly_scheme.auth_seq_num 101
_pdbx_nonpoly_scheme.pdb_mon_id FMT
_pdbx_nonpoly_scheme.auth_mon_id FMT
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
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 ? ? ? 5.8.0267 1
? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? 2.2.10 2
? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? 2.2.10 3
? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 2.8.3 4
? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? 0.9.6 5
#
_cell.angle_alpha 90.00
_cell.angle_alpha_esd ?
_cell.angle_beta 88.60
_cell.angle_beta_esd ?
_cell.angle_gamma 90.00
_cell.angle_gamma_esd ?
_cell.entry_id 8YG2
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 4.864
_cell.length_a_esd ?
_cell.length_b 20.466
_cell.length_b_esd ?
_cell.length_c 20.855
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB 2
_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 ?
_cell.pdbx_esd_method ?
#
_symmetry.entry_id 8YG2
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 4
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 1 21 1'
_symmetry.pdbx_full_space_group_name_H-M ?
#
_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 8YG2
_exptl.crystals_number 1
_exptl.details ?
_exptl.method 'X-RAY DIFFRACTION'
_exptl.method_details ?
#
_exptl_crystal.colour ?
_exptl_crystal.density_diffrn ?
_exptl_crystal.density_Matthews 1.54
_exptl_crystal.density_method ?
_exptl_crystal.density_percent_sol 15.15
_exptl_crystal.description Needle
_exptl_crystal.F_000 ?
_exptl_crystal.id 1
_exptl_crystal.preparation ?
_exptl_crystal.size_max ?
_exptl_crystal.size_mid ?
_exptl_crystal.size_min ?
_exptl_crystal.size_rad ?
_exptl_crystal.colour_lustre ?
_exptl_crystal.colour_modifier ?
_exptl_crystal.colour_primary ?
_exptl_crystal.density_meas ?
_exptl_crystal.density_meas_esd ?
_exptl_crystal.density_meas_gt ?
_exptl_crystal.density_meas_lt ?
_exptl_crystal.density_meas_temp ?
_exptl_crystal.density_meas_temp_esd ?
_exptl_crystal.density_meas_temp_gt ?
_exptl_crystal.density_meas_temp_lt ?
_exptl_crystal.pdbx_crystal_image_url ?
_exptl_crystal.pdbx_crystal_image_format ?
_exptl_crystal.pdbx_mosaicity ?
_exptl_crystal.pdbx_mosaicity_esd ?
_exptl_crystal.pdbx_mosaic_method ?
_exptl_crystal.pdbx_mosaic_block_size ?
_exptl_crystal.pdbx_mosaic_block_size_esd ?
#
_exptl_crystal_grow.apparatus ?
_exptl_crystal_grow.atmosphere ?
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.details ?
_exptl_crystal_grow.method EVAPORATION
_exptl_crystal_grow.method_ref ?
_exptl_crystal_grow.pH ?
_exptl_crystal_grow.pressure ?
_exptl_crystal_grow.pressure_esd ?
_exptl_crystal_grow.seeding ?
_exptl_crystal_grow.seeding_ref ?
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.temp_esd ?
_exptl_crystal_grow.time ?
_exptl_crystal_grow.pdbx_details 'Formic acid'
_exptl_crystal_grow.pdbx_pH_range 2.0-3.0
_exptl_crystal_grow.temp 298
#
_diffrn.ambient_environment ?
_diffrn.ambient_temp 100
_diffrn.ambient_temp_details ?
_diffrn.ambient_temp_esd ?
_diffrn.crystal_id 1
_diffrn.crystal_support ?
_diffrn.crystal_treatment ?
_diffrn.details ?
_diffrn.id 1
_diffrn.ambient_pressure ?
_diffrn.ambient_pressure_esd ?
_diffrn.ambient_pressure_gt ?
_diffrn.ambient_pressure_lt ?
_diffrn.ambient_temp_gt ?
_diffrn.ambient_temp_lt ?
_diffrn.pdbx_serial_crystal_experiment N
#
_diffrn_detector.details ?
_diffrn_detector.detector PIXEL
_diffrn_detector.diffrn_id 1
_diffrn_detector.type 'DECTRIS EIGER X 4M'
_diffrn_detector.area_resol_mean ?
_diffrn_detector.dtime ?
_diffrn_detector.pdbx_frames_total ?
_diffrn_detector.pdbx_collection_time_total ?
_diffrn_detector.pdbx_collection_date 2022-10-21
_diffrn_detector.pdbx_frequency ?
_diffrn_detector.id ?
_diffrn_detector.number_of_axes ?
#
_diffrn_radiation.collimation ?
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.filter_edge ?
_diffrn_radiation.inhomogeneity ?
_diffrn_radiation.monochromator ?
_diffrn_radiation.polarisn_norm ?
_diffrn_radiation.polarisn_ratio ?
_diffrn_radiation.probe ?
_diffrn_radiation.type ?
_diffrn_radiation.xray_symbol ?
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.pdbx_wavelength_list ?
_diffrn_radiation.pdbx_wavelength ?
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_analyzer ?
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.040
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.current ?
_diffrn_source.details ?
_diffrn_source.diffrn_id 1
_diffrn_source.power ?
_diffrn_source.size ?
_diffrn_source.source SYNCHROTRON
_diffrn_source.target ?
_diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-1A'
_diffrn_source.voltage ?
_diffrn_source.take-off_angle ?
_diffrn_source.pdbx_wavelength_list 1.040
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_synchrotron_beamline BL-1A
_diffrn_source.pdbx_synchrotron_site 'Photon Factory'
#
_reflns.B_iso_Wilson_estimate ?
_reflns.entry_id 8YG2
_reflns.data_reduction_details ?
_reflns.data_reduction_method ?
_reflns.d_resolution_high 1.250
_reflns.d_resolution_low 20.470
_reflns.details ?
_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_obs 1063
_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.percent_possible_obs 91.9
_reflns.R_free_details ?
_reflns.Rmerge_F_all ?
_reflns.Rmerge_F_obs ?
_reflns.Friedel_coverage ?
_reflns.number_gt ?
_reflns.threshold_expression ?
_reflns.pdbx_redundancy 2.000
_reflns.pdbx_netI_over_av_sigmaI ?
_reflns.pdbx_netI_over_sigmaI 59.1100
_reflns.pdbx_res_netI_over_av_sigmaI_2 ?
_reflns.pdbx_res_netI_over_sigmaI_2 ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_d_res_high_opt ?
_reflns.pdbx_d_res_low_opt ?
_reflns.pdbx_d_res_opt_method ?
_reflns.phase_calculation_details ?
_reflns.pdbx_Rrim_I_all ?
_reflns.pdbx_Rpim_I_all ?
_reflns.pdbx_d_opt ?
_reflns.pdbx_number_measured_all ?
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.pdbx_CC_half ?
_reflns.pdbx_CC_star ?
_reflns.pdbx_R_split ?
_reflns.pdbx_Rmerge_I_obs 0.08400
_reflns.pdbx_Rmerge_I_all ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_CC_split_method ?
_reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ?
_reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ?
_reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ?
_reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ?
_reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ?
_reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ?
_reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ?
_reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ?
_reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ?
_reflns.pdbx_aniso_diffraction_limit_1 ?
_reflns.pdbx_aniso_diffraction_limit_2 ?
_reflns.pdbx_aniso_diffraction_limit_3 ?
_reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ?
_reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ?
_reflns.pdbx_aniso_B_tensor_eigenvalue_1 ?
_reflns.pdbx_aniso_B_tensor_eigenvalue_2 ?
_reflns.pdbx_aniso_B_tensor_eigenvalue_3 ?
_reflns.pdbx_orthogonalization_convention ?
_reflns.pdbx_percent_possible_ellipsoidal ?
_reflns.pdbx_percent_possible_spherical ?
_reflns.pdbx_percent_possible_ellipsoidal_anomalous ?
_reflns.pdbx_percent_possible_spherical_anomalous ?
_reflns.pdbx_redundancy_anomalous ?
_reflns.pdbx_CC_half_anomalous ?
_reflns.pdbx_absDiff_over_sigma_anomalous ?
_reflns.pdbx_percent_possible_anomalous ?
_reflns.pdbx_observed_signal_threshold ?
_reflns.pdbx_signal_type ?
_reflns.pdbx_signal_details ?
_reflns.pdbx_signal_software_id ?
#
_reflns_shell.d_res_high 1.25
_reflns_shell.d_res_low 1.27
_reflns_shell.meanI_over_sigI_all ?
_reflns_shell.meanI_over_sigI_obs ?
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_possible ?
_reflns_shell.number_unique_all ?
_reflns_shell.number_unique_obs 55
_reflns_shell.percent_possible_obs ?
_reflns_shell.Rmerge_F_all ?
_reflns_shell.Rmerge_F_obs ?
_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 2.00
_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 1
_reflns_shell.pdbx_CC_half ?
_reflns_shell.pdbx_CC_star ?
_reflns_shell.pdbx_R_split ?
_reflns_shell.percent_possible_all 94.8
_reflns_shell.Rmerge_I_all ?
_reflns_shell.Rmerge_I_obs 0.15500
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.pdbx_percent_possible_ellipsoidal ?
_reflns_shell.pdbx_percent_possible_spherical ?
_reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ?
_reflns_shell.pdbx_percent_possible_spherical_anomalous ?
_reflns_shell.pdbx_redundancy_anomalous ?
_reflns_shell.pdbx_CC_half_anomalous ?
_reflns_shell.pdbx_absDiff_over_sigma_anomalous ?
_reflns_shell.pdbx_percent_possible_anomalous ?
#
_refine.aniso_B[1][1] -0.11500
_refine.aniso_B[1][2] 0.00000
_refine.aniso_B[1][3] 0.18900
_refine.aniso_B[2][2] -0.01100
_refine.aniso_B[2][3] 0.00000
_refine.aniso_B[3][3] 0.13500
_refine.B_iso_max ?
_refine.B_iso_mean 5.94
_refine.B_iso_min ?
_refine.correlation_coeff_Fo_to_Fc 0.963
_refine.correlation_coeff_Fo_to_Fc_free 0.951
_refine.details ?
_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 8YG2
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_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 1.25
_refine.ls_d_res_low 20.47
_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 1054
_refine.ls_number_reflns_R_free 63
_refine.ls_number_reflns_R_work ?
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 91.1
_refine.ls_percent_reflns_R_free 5.977
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_R_free 0.201
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work 0.174
_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 'MASK BULK SOLVENT'
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.pdbx_R_complete ?
_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 'FREE R-VALUE'
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_starting_model ?
_refine.pdbx_stereochemistry_target_values ?
_refine.pdbx_R_Free_selection_details ?
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_overall_ESU_R 0.070
_refine.pdbx_overall_ESU_R_Free 0.069
_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 0.881
_refine.overall_SU_ML 0.035
_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 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.details ?
_refine_hist.d_res_high 1.25
_refine_hist.d_res_low 20.47
_refine_hist.number_atoms_solvent 0
_refine_hist.number_atoms_total 54
_refine_hist.number_reflns_all ?
_refine_hist.number_reflns_obs ?
_refine_hist.number_reflns_R_free ?
_refine_hist.number_reflns_R_work ?
_refine_hist.R_factor_all ?
_refine_hist.R_factor_obs ?
_refine_hist.R_factor_R_free ?
_refine_hist.R_factor_R_work ?
_refine_hist.pdbx_number_residues_total ?
_refine_hist.pdbx_B_iso_mean_ligand ?
_refine_hist.pdbx_B_iso_mean_solvent ?
_refine_hist.pdbx_number_atoms_protein 51
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 3
_refine_hist.pdbx_number_atoms_lipid ?
_refine_hist.pdbx_number_atoms_carb ?
_refine_hist.pdbx_pseudo_atom_details ?
#
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
'X-RAY DIFFRACTION' ? 0.009 0.014 67 ? r_bond_refined_d ? ?
'X-RAY DIFFRACTION' ? 0.003 0.018 75 ? r_bond_other_d ? ?
'X-RAY DIFFRACTION' ? 1.733 1.920 82 ? r_angle_refined_deg ? ?
'X-RAY DIFFRACTION' ? 1.045 2.001 157 ? r_angle_other_deg ? ?
'X-RAY DIFFRACTION' ? 3.777 5.000 6 ? r_dihedral_angle_1_deg ? ?
'X-RAY DIFFRACTION' ? 44.446 26.667 3 ? r_dihedral_angle_2_deg ? ?
'X-RAY DIFFRACTION' ? 14.912 15.000 5 ? r_dihedral_angle_3_deg ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ?
'X-RAY DIFFRACTION' ? 0.043 0.200 6 ? r_chiral_restr ? ?
'X-RAY DIFFRACTION' ? 0.005 0.020 81 ? r_gen_planes_refined ? ?
'X-RAY DIFFRACTION' ? 0.002 0.020 30 ? r_gen_planes_other ? ?
'X-RAY DIFFRACTION' ? 0.014 0.200 3 ? r_nbd_refined ? ?
'X-RAY DIFFRACTION' ? 0.203 0.200 37 ? r_nbd_other ? ?
'X-RAY DIFFRACTION' ? 0.187 0.200 22 ? r_nbtor_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ?
'X-RAY DIFFRACTION' ? 0.030 0.200 1 ? r_xyhbond_nbd_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ?
'X-RAY DIFFRACTION' ? 0.230 0.543 23 ? r_mcbond_it ? ?
'X-RAY DIFFRACTION' ? 0.231 0.650 24 ? r_mcbond_other ? ?
'X-RAY DIFFRACTION' ? 0.376 0.817 26 ? r_mcangle_it ? ?
'X-RAY DIFFRACTION' ? 0.380 0.825 27 ? r_mcangle_other ? ?
'X-RAY DIFFRACTION' ? 0.206 0.674 44 ? r_scbond_it ? ?
'X-RAY DIFFRACTION' ? 0.205 0.563 43 ? r_scbond_other ? ?
'X-RAY DIFFRACTION' ? 0.220 0.885 52 ? r_scangle_it ? ?
'X-RAY DIFFRACTION' ? 0.219 0.956 53 ? r_scangle_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_refined ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_other ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ?
'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ?
#
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_ls_shell.d_res_high 1.25
_refine_ls_shell.d_res_low 1.28
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.number_reflns_R_free 1
_refine_ls_shell.number_reflns_R_work 74
_refine_ls_shell.percent_reflns_obs 94.94
_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_error ?
_refine_ls_shell.R_factor_R_work 0.2430
_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_R_complete ?
_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 ?
_refine_ls_shell.R_factor_R_free 0.2630
#
_struct.entry_id 8YG2
_struct.title 'Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide'
_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 8YG2
_struct_keywords.text 'Amyloid, CASL, Protein fibril'
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
#
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 ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 8YG2
_struct_ref.pdbx_db_accession 8YG2
_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 8YG2
_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 8
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 8YG2
_struct_ref_seq.db_align_beg 0
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 7
_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 7
#
_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
#
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)' 180 ?
1 MORE 0 ?
1 'SSA (A^2)' 1180 ?
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B
#
_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 ?
#
_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_
_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 PIV 1 C A ? ? 1_555 A ASN 2 N A ? A PIV 0 A ASN 1 1_555 ? ? ? ? ? ? ? 1.348 ? ?
covale2 covale both ? A PIV 1 C B ? ? 1_555 A ASN 2 N B ? A PIV 0 A ASN 1 1_555 ? ? ? ? ? ? ? 1.341 ? ?
covale3 covale both ? A LEU 7 C ? ? ? 1_555 A NH2 8 N ? ? A LEU 6 A NH2 7 1_555 ? ? ? ? ? ? ? 1.331 ? ?
#
_struct_conn_type.id covale
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.label_alt_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.modified_residue_label_alt_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.symmetry
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.modified_residue_symmetry
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
1 PIV A 1 A . . . . PIV A 0 ? 1_555 . . . . . . . ? 1 PIV None 'Non-standard residue'
2 PIV A 1 B . . . . PIV A 0 ? 1_555 . . . . . . . ? 1 PIV None 'Non-standard residue'
3 NH2 A 8 ? LEU A 7 ? NH2 A 7 ? 1_555 LEU A 6 ? 1_555 . . LEU 14 NH2 None 'Terminal amidation'
#
_pdbx_entry_details.entry_id 8YG2
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.has_ligand_of_interest N
_pdbx_entry_details.has_protein_modification Y
#
loop_
_pdbx_validate_rmsd_bond.id
_pdbx_validate_rmsd_bond.PDB_model_num
_pdbx_validate_rmsd_bond.auth_atom_id_1
_pdbx_validate_rmsd_bond.auth_asym_id_1
_pdbx_validate_rmsd_bond.auth_comp_id_1
_pdbx_validate_rmsd_bond.auth_seq_id_1
_pdbx_validate_rmsd_bond.PDB_ins_code_1
_pdbx_validate_rmsd_bond.label_alt_id_1
_pdbx_validate_rmsd_bond.auth_atom_id_2
_pdbx_validate_rmsd_bond.auth_asym_id_2
_pdbx_validate_rmsd_bond.auth_comp_id_2
_pdbx_validate_rmsd_bond.auth_seq_id_2
_pdbx_validate_rmsd_bond.PDB_ins_code_2
_pdbx_validate_rmsd_bond.label_alt_id_2
_pdbx_validate_rmsd_bond.bond_value
_pdbx_validate_rmsd_bond.bond_target_value
_pdbx_validate_rmsd_bond.bond_deviation
_pdbx_validate_rmsd_bond.bond_standard_deviation
_pdbx_validate_rmsd_bond.linker_flag
1 1 N A ASN 1 ? A CA A ASN 1 ? A 1.309 1.459 -0.150 0.020 N
2 1 N A ASN 1 ? B CA A ASN 1 ? B 1.279 1.459 -0.180 0.020 N
#
_pdbx_validate_rmsd_angle.id 1
_pdbx_validate_rmsd_angle.PDB_model_num 1
_pdbx_validate_rmsd_angle.auth_atom_id_1 N
_pdbx_validate_rmsd_angle.auth_asym_id_1 A
_pdbx_validate_rmsd_angle.auth_comp_id_1 ASN
_pdbx_validate_rmsd_angle.auth_seq_id_1 1
_pdbx_validate_rmsd_angle.PDB_ins_code_1 ?
_pdbx_validate_rmsd_angle.label_alt_id_1 B
_pdbx_validate_rmsd_angle.auth_atom_id_2 CA
_pdbx_validate_rmsd_angle.auth_asym_id_2 A
_pdbx_validate_rmsd_angle.auth_comp_id_2 ASN
_pdbx_validate_rmsd_angle.auth_seq_id_2 1
_pdbx_validate_rmsd_angle.PDB_ins_code_2 ?
_pdbx_validate_rmsd_angle.label_alt_id_2 B
_pdbx_validate_rmsd_angle.auth_atom_id_3 CB
_pdbx_validate_rmsd_angle.auth_asym_id_3 A
_pdbx_validate_rmsd_angle.auth_comp_id_3 ASN
_pdbx_validate_rmsd_angle.auth_seq_id_3 1
_pdbx_validate_rmsd_angle.PDB_ins_code_3 ?
_pdbx_validate_rmsd_angle.label_alt_id_3 B
_pdbx_validate_rmsd_angle.angle_value 122.62
_pdbx_validate_rmsd_angle.angle_target_value 110.60
_pdbx_validate_rmsd_angle.angle_deviation 12.02
_pdbx_validate_rmsd_angle.angle_standard_deviation 1.80
_pdbx_validate_rmsd_angle.linker_flag N
#
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
ASN N N N N 14
ASN CA C N S 15
ASN C C N N 16
ASN O O N N 17
ASN CB C N N 18
ASN CG C N N 19
ASN OD1 O N N 20
ASN ND2 N N N 21
ASN OXT O N N 22
ASN H H N N 23
ASN H2 H N N 24
ASN HA H N N 25
ASN HB2 H N N 26
ASN HB3 H N N 27
ASN HD21 H N N 28
ASN HD22 H N N 29
ASN HXT H N N 30
FMT C C N N 31
FMT O1 O N N 32
FMT O2 O N N 33
FMT H H N N 34
FMT HO2 H N N 35
GLY N N N N 36
GLY CA C N N 37
GLY C C N N 38
GLY O O N N 39
GLY OXT O N N 40
GLY H H N N 41
GLY H2 H N N 42
GLY HA2 H N N 43
GLY HA3 H N N 44
GLY HXT H N N 45
ILE N N N N 46
ILE CA C N S 47
ILE C C N N 48
ILE O O N N 49
ILE CB C N S 50
ILE CG1 C N N 51
ILE CG2 C N N 52
ILE CD1 C N N 53
ILE OXT O N N 54
ILE H H N N 55
ILE H2 H N N 56
ILE HA H N N 57
ILE HB H N N 58
ILE HG12 H N N 59
ILE HG13 H N N 60
ILE HG21 H N N 61
ILE HG22 H N N 62
ILE HG23 H N N 63
ILE HD11 H N N 64
ILE HD12 H N N 65
ILE HD13 H N N 66
ILE HXT H N N 67
LEU N N N N 68
LEU CA C N S 69
LEU C C N N 70
LEU O O N N 71
LEU CB C N N 72
LEU CG C N N 73
LEU CD1 C N N 74
LEU CD2 C N N 75
LEU OXT O N N 76
LEU H H N N 77
LEU H2 H N N 78
LEU HA H N N 79
LEU HB2 H N N 80
LEU HB3 H N N 81
LEU HG H N N 82
LEU HD11 H N N 83
LEU HD12 H N N 84
LEU HD13 H N N 85
LEU HD21 H N N 86
LEU HD22 H N N 87
LEU HD23 H N N 88
LEU HXT H N N 89
NH2 N N N N 90
NH2 HN1 H N N 91
NH2 HN2 H N N 92
PHE N N N N 93
PHE CA C N S 94
PHE C C N N 95
PHE O O N N 96
PHE CB C N N 97
PHE CG C Y N 98
PHE CD1 C Y N 99
PHE CD2 C Y N 100
PHE CE1 C Y N 101
PHE CE2 C Y N 102
PHE CZ C Y N 103
PHE OXT O N N 104
PHE H H N N 105
PHE H2 H N N 106
PHE HA H N N 107
PHE HB2 H N N 108
PHE HB3 H N N 109
PHE HD1 H N N 110
PHE HD2 H N N 111
PHE HE1 H N N 112
PHE HE2 H N N 113
PHE HZ H N N 114
PHE HXT H N N 115
PIV CT C N N 116
PIV C1 C N N 117
PIV C2 C N N 118
PIV C3 C N N 119
PIV C C N N 120
PIV O1 O N N 121
PIV O2 O N N 122
PIV H11 H N N 123
PIV H12 H N N 124
PIV H13 H N N 125
PIV H21 H N N 126
PIV H22 H N N 127
PIV H23 H N N 128
PIV H31 H N N 129
PIV H32 H N N 130
PIV H33 H N N 131
PIV HO2 H N N 132
#
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
ASN N CA sing N N 13
ASN N H sing N N 14
ASN N H2 sing N N 15
ASN CA C sing N N 16
ASN CA CB sing N N 17
ASN CA HA sing N N 18
ASN C O doub N N 19
ASN C OXT sing N N 20
ASN CB CG sing N N 21
ASN CB HB2 sing N N 22
ASN CB HB3 sing N N 23
ASN CG OD1 doub N N 24
ASN CG ND2 sing N N 25
ASN ND2 HD21 sing N N 26
ASN ND2 HD22 sing N N 27
ASN OXT HXT sing N N 28
FMT C O1 doub N N 29
FMT C O2 sing N N 30
FMT C H sing N N 31
FMT O2 HO2 sing N N 32
GLY N CA sing N N 33
GLY N H sing N N 34
GLY N H2 sing N N 35
GLY CA C sing N N 36
GLY CA HA2 sing N N 37
GLY CA HA3 sing N N 38
GLY C O doub N N 39
GLY C OXT sing N N 40
GLY OXT HXT sing N N 41
ILE N CA sing N N 42
ILE N H sing N N 43
ILE N H2 sing N N 44
ILE CA C sing N N 45
ILE CA CB sing N N 46
ILE CA HA sing N N 47
ILE C O doub N N 48
ILE C OXT sing N N 49
ILE CB CG1 sing N N 50
ILE CB CG2 sing N N 51
ILE CB HB sing N N 52
ILE CG1 CD1 sing N N 53
ILE CG1 HG12 sing N N 54
ILE CG1 HG13 sing N N 55
ILE CG2 HG21 sing N N 56
ILE CG2 HG22 sing N N 57
ILE CG2 HG23 sing N N 58
ILE CD1 HD11 sing N N 59
ILE CD1 HD12 sing N N 60
ILE CD1 HD13 sing N N 61
ILE OXT HXT sing N N 62
LEU N CA sing N N 63
LEU N H sing N N 64
LEU N H2 sing N N 65
LEU CA C sing N N 66
LEU CA CB sing N N 67
LEU CA HA sing N N 68
LEU C O doub N N 69
LEU C OXT sing N N 70
LEU CB CG sing N N 71
LEU CB HB2 sing N N 72
LEU CB HB3 sing N N 73
LEU CG CD1 sing N N 74
LEU CG CD2 sing N N 75
LEU CG HG sing N N 76
LEU CD1 HD11 sing N N 77
LEU CD1 HD12 sing N N 78
LEU CD1 HD13 sing N N 79
LEU CD2 HD21 sing N N 80
LEU CD2 HD22 sing N N 81
LEU CD2 HD23 sing N N 82
LEU OXT HXT sing N N 83
NH2 N HN1 sing N N 84
NH2 N HN2 sing N N 85
PHE N CA sing N N 86
PHE N H sing N N 87
PHE N H2 sing N N 88
PHE CA C sing N N 89
PHE CA CB sing N N 90
PHE CA HA sing N N 91
PHE C O doub N N 92
PHE C OXT sing N N 93
PHE CB CG sing N N 94
PHE CB HB2 sing N N 95
PHE CB HB3 sing N N 96
PHE CG CD1 doub Y N 97
PHE CG CD2 sing Y N 98
PHE CD1 CE1 sing Y N 99
PHE CD1 HD1 sing N N 100
PHE CD2 CE2 doub Y N 101
PHE CD2 HD2 sing N N 102
PHE CE1 CZ doub Y N 103
PHE CE1 HE1 sing N N 104
PHE CE2 CZ sing Y N 105
PHE CE2 HE2 sing N N 106
PHE CZ HZ sing N N 107
PHE OXT HXT sing N N 108
PIV CT C1 sing N N 109
PIV CT C2 sing N N 110
PIV CT C3 sing N N 111
PIV CT C sing N N 112
PIV C1 H11 sing N N 113
PIV C1 H12 sing N N 114
PIV C1 H13 sing N N 115
PIV C2 H21 sing N N 116
PIV C2 H22 sing N N 117
PIV C2 H23 sing N N 118
PIV C3 H31 sing N N 119
PIV C3 H32 sing N N 120
PIV C3 H33 sing N N 121
PIV C O1 doub N N 122
PIV C O2 sing N N 123
PIV O2 HO2 sing N N 124
#
_pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)'
_pdbx_audit_support.country Japan
_pdbx_audit_support.grant_number ?
_pdbx_audit_support.ordinal 1
#
_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 3DGJ
_pdbx_initial_refinement_model.details ?
#
_atom_sites.entry_id 8YG2
_atom_sites.Cartn_transf_matrix[1][1] ?
_atom_sites.Cartn_transf_matrix[1][2] ?
_atom_sites.Cartn_transf_matrix[1][3] ?
_atom_sites.Cartn_transf_matrix[2][1] ?
_atom_sites.Cartn_transf_matrix[2][2] ?
_atom_sites.Cartn_transf_matrix[2][3] ?
_atom_sites.Cartn_transf_matrix[3][1] ?
_atom_sites.Cartn_transf_matrix[3][2] ?
_atom_sites.Cartn_transf_matrix[3][3] ?
_atom_sites.Cartn_transf_vector[1] ?
_atom_sites.Cartn_transf_vector[2] ?
_atom_sites.Cartn_transf_vector[3] ?
_atom_sites.Cartn_transform_axes ?
_atom_sites.fract_transf_matrix[1][1] 0.205592
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] -0.005028
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.048862
_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] 0.047964
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
_atom_sites.solution_primary ?
_atom_sites.solution_secondary ?
_atom_sites.solution_hydrogens ?
_atom_sites.special_details ?
#
loop_
_atom_type.symbol
_atom_type.pdbx_scat_Z
_atom_type.pdbx_N_electrons
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b4
C 6 6 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651
H 1 1 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800
N 7 7 12.222 0.006 3.135 9.893 2.014 28.997 1.167 0.583
O 8 8 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909
#
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
_atom_site.calc_flag
HETATM 1 C CT A PIV A 1 1 ? -1.817 -11.745 4.357 0.70 6.02 0 0 PIV A CT 1 ?
HETATM 2 C CT B PIV A 1 1 ? -1.798 -12.032 5.428 0.30 4.43 0 0 PIV A CT 1 ?
HETATM 3 C C1 A PIV A 1 1 ? -0.789 -12.716 3.814 0.70 6.03 0 0 PIV A C1 1 ?
HETATM 4 C C1 B PIV A 1 1 ? -2.096 -12.107 3.929 0.30 4.42 0 0 PIV A C1 1 ?
HETATM 5 C C2 A PIV A 1 1 ? -2.413 -12.389 5.598 0.70 6.02 0 0 PIV A C2 1 ?
HETATM 6 C C2 B PIV A 1 1 ? -0.792 -13.129 5.781 0.30 4.39 0 0 PIV A C2 1 ?
HETATM 7 C C3 A PIV A 1 1 ? -2.829 -11.569 3.228 0.70 6.00 0 0 PIV A C3 1 ?
HETATM 8 C C3 B PIV A 1 1 ? -3.090 -12.199 6.225 0.30 4.44 0 0 PIV A C3 1 ?
HETATM 9 C C A PIV A 1 1 ? -1.224 -10.401 4.786 0.70 5.94 0 0 PIV A C 1 ?
HETATM 10 C C B PIV A 1 1 ? -1.201 -10.679 5.751 0.30 4.49 0 0 PIV A C 1 ?
HETATM 11 O O1 A PIV A 1 1 ? -0.060 -10.112 4.546 0.70 6.05 0 0 PIV A O1 1 ?
HETATM 12 O O1 B PIV A 1 1 ? -0.014 -10.603 6.046 0.30 4.46 0 0 PIV A O1 1 ?
ATOM 13 N N A ASN A 1 2 ? -1.962 -9.494 5.456 0.70 5.62 0 1 ASN A N 1 ?
ATOM 14 N N B ASN A 1 2 ? -1.974 -9.584 5.710 0.30 4.62 0 1 ASN A N 1 ?
ATOM 15 C CA A ASN A 1 2 ? -1.556 -8.294 5.787 0.70 4.82 0 1 ASN A CA 1 ?
ATOM 16 C CA B ASN A 1 2 ? -1.723 -8.334 5.814 0.30 4.98 0 1 ASN A CA 1 ?
ATOM 17 C C A ASN A 1 2 ? -1.968 -7.852 7.197 0.70 4.89 0 1 ASN A C 1 ?
ATOM 18 C C B ASN A 1 2 ? -2.007 -7.920 7.262 0.30 5.02 0 1 ASN A C 1 ?
ATOM 19 O O A ASN A 1 2 ? -3.172 -7.809 7.480 0.70 5.00 0 1 ASN A O 1 ?
ATOM 20 O O B ASN A 1 2 ? -3.184 -7.990 7.660 0.30 5.06 0 1 ASN A O 1 ?
ATOM 21 C CB A ASN A 1 2 ? -1.977 -7.183 4.817 0.70 4.53 0 1 ASN A CB 1 ?
ATOM 22 C CB B ASN A 1 2 ? -2.302 -7.291 4.849 0.30 5.09 0 1 ASN A CB 1 ?
ATOM 23 C CG A ASN A 1 2 ? -1.462 -5.822 5.231 0.70 4.30 0 1 ASN A CG 1 ?
ATOM 24 C CG B ASN A 1 2 ? -3.775 -7.003 5.072 0.30 5.14 0 1 ASN A CG 1 ?
ATOM 25 O OD1 A ASN A 1 2 ? -0.256 -5.611 5.322 0.70 3.98 0 1 ASN A OD1 1 ?
ATOM 26 O OD1 B ASN A 1 2 ? -4.597 -7.917 5.137 0.30 5.27 0 1 ASN A OD1 1 ?
ATOM 27 N ND2 A ASN A 1 2 ? -2.366 -4.882 5.437 0.70 4.21 0 1 ASN A ND2 1 ?
ATOM 28 N ND2 B ASN A 1 2 ? -4.125 -5.729 5.167 0.30 5.15 0 1 ASN A ND2 1 ?
ATOM 29 N N . PHE A 1 3 ? -0.978 -7.520 8.018 1.00 4.96 0 2 PHE A N 1 ?
ATOM 30 C CA . PHE A 1 3 ? -1.135 -7.032 9.410 1.00 5.12 0 2 PHE A CA 1 ?
ATOM 31 C C . PHE A 1 3 ? -0.569 -5.618 9.535 1.00 5.19 0 2 PHE A C 1 ?
ATOM 32 O O . PHE A 1 3 ? -0.759 -4.998 10.583 1.00 5.78 0 2 PHE A O 1 ?
ATOM 33 C CB . PHE A 1 3 ? -0.435 -7.999 10.359 1.00 5.05 0 2 PHE A CB 1 ?
ATOM 34 C CG . PHE A 1 3 ? -1.061 -9.369 10.354 1.00 5.06 0 2 PHE A CG 1 ?
ATOM 35 C CD1 . PHE A 1 3 ? -2.159 -9.642 11.153 1.00 5.07 0 2 PHE A CD1 1 ?
ATOM 36 C CD2 . PHE A 1 3 ? -0.584 -10.369 9.520 1.00 4.94 0 2 PHE A CD2 1 ?
ATOM 37 C CE1 . PHE A 1 3 ? -2.739 -10.899 11.151 1.00 5.11 0 2 PHE A CE1 1 ?
ATOM 38 C CE2 . PHE A 1 3 ? -1.168 -11.626 9.521 1.00 5.01 0 2 PHE A CE2 1 ?
ATOM 39 C CZ . PHE A 1 3 ? -2.253 -11.884 10.324 1.00 5.02 0 2 PHE A CZ 1 ?
ATOM 40 N N . GLY A 1 4 ? 0.066 -5.118 8.475 1.00 5.11 0 3 GLY A N 1 ?
ATOM 41 C CA . GLY A 1 4 ? 0.762 -3.824 8.454 1.00 5.02 0 3 GLY A CA 1 ?
ATOM 42 C C . GLY A 1 4 ? 0.083 -2.848 7.507 1.00 5.11 0 3 GLY A C 1 ?
ATOM 43 O O . GLY A 1 4 ? -1.145 -2.946 7.292 1.00 4.75 0 3 GLY A O 1 ?
ATOM 44 N N . ALA A 1 5 ? 0.866 -1.922 6.970 1.00 5.34 0 4 ALA A N 1 ?
ATOM 45 C CA . ALA A 1 5 ? 0.396 -0.889 6.026 1.00 5.56 0 4 ALA A CA 1 ?
ATOM 46 C C . ALA A 1 5 ? 0.998 -1.162 4.645 1.00 5.64 0 4 ALA A C 1 ?
ATOM 47 O O . ALA A 1 5 ? 2.231 -1.327 4.543 1.00 5.63 0 4 ALA A O 1 ?
ATOM 48 C CB . ALA A 1 5 ? 0.760 0.475 6.550 1.00 5.58 0 4 ALA A CB 1 ?
ATOM 49 N N . ILE A 1 6 ? 0.148 -1.225 3.619 1.00 5.88 0 5 ILE A N 1 ?
ATOM 50 C CA . ILE A 1 6 ? 0.588 -1.352 2.202 1.00 6.16 0 5 ILE A CA 1 ?
ATOM 51 C C . ILE A 1 6 ? 0.042 -0.142 1.446 1.00 6.26 0 5 ILE A C 1 ?
ATOM 52 O O . ILE A 1 6 ? -1.204 0.027 1.381 1.00 6.13 0 5 ILE A O 1 ?
ATOM 53 C CB . ILE A 1 6 ? 0.157 -2.696 1.584 1.00 6.25 0 5 ILE A CB 1 ?
ATOM 54 C CG1 . ILE A 1 6 ? 0.761 -3.869 2.360 1.00 6.30 0 5 ILE A CG1 1 ?
ATOM 55 C CG2 . ILE A 1 6 ? 0.529 -2.753 0.112 1.00 6.22 0 5 ILE A CG2 1 ?
ATOM 56 C CD1 . ILE A 1 6 ? 0.288 -5.233 1.897 1.00 6.36 0 5 ILE A CD1 1 ?
ATOM 57 N N . LEU A 1 7 ? 0.960 0.705 0.975 1.00 6.61 0 6 LEU A N 1 ?
ATOM 58 C CA . LEU A 1 7 ? 0.663 1.983 0.268 1.00 7.12 0 6 LEU A CA 1 ?
ATOM 59 C C . LEU A 1 7 ? 0.822 1.732 -1.176 1.00 7.70 0 6 LEU A C 1 ?
ATOM 60 O O . LEU A 1 7 ? 2.008 1.685 -1.561 1.00 7.97 0 6 LEU A O 1 ?
ATOM 61 C CB . LEU A 1 7 ? 1.486 3.109 0.899 1.00 7.26 0 6 LEU A CB 1 ?
ATOM 62 C CG . LEU A 1 7 ? 0.799 3.887 2.020 1.00 7.52 0 6 LEU A CG 1 ?
ATOM 63 C CD1 . LEU A 1 7 ? 0.376 2.990 3.176 1.00 7.48 0 6 LEU A CD1 1 ?
ATOM 64 C CD2 . LEU A 1 7 ? 1.717 4.986 2.516 1.00 7.49 0 6 LEU A CD2 1 ?
HETATM 65 N N . NH2 A 1 8 ? -0.197 1.444 -1.983 1.00 7.97 0 7 NH2 A N 1 ?
HETATM 66 C C . FMT B 2 . ? -3.082 -6.190 12.659 1.00 31.19 0 101 FMT A C 1 ?
HETATM 67 O O1 . FMT B 2 . ? -3.001 -6.505 13.828 1.00 31.43 0 101 FMT A O1 1 ?
HETATM 68 O O2 . FMT B 2 . ? -2.935 -4.986 12.197 1.00 31.09 0 101 FMT A O2 1 ?
#