data_8T89
#
_entry.id 8T89
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.382
_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 8T89 pdb_00008t89 10.2210/pdb8t89/pdb
WWPDB D_1000275465 ? ?
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 8T89
_pdbx_database_status.recvd_initial_deposition_date 2023-06-22
_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.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Sawaya, M.R.' 1 0000-0003-0874-9043
'Raskatov, J.A.' 2 0000-0002-0082-9113
'Hazari, A.' 3 0009-0005-2071-1322
#
_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 J.Am.Chem.Soc.
_citation.journal_id_ASTM JACSAT
_citation.journal_id_CSD ?
_citation.journal_id_ISSN 1520-5126
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume 145
_citation.language ?
_citation.page_first 25917
_citation.page_last 25926
_citation.title
'Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.'
_citation.year 2023
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1021/jacs.3c11712
_citation.pdbx_database_id_PubMed 37972334
_citation.pdbx_database_id_patent ?
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Hazari, A.' 1 ?
primary 'Sawaya, M.R.' 2 ?
primary 'Sajimon, M.' 3 ?
primary 'Vlahakis, N.' 4 ?
primary 'Rodriguez, J.' 5 ?
primary 'Eisenberg, D.' 6 ?
primary 'Raskatov, J.A.' 7 ?
#
_cell.angle_alpha 89.955
_cell.angle_alpha_esd ?
_cell.angle_beta 91.778
_cell.angle_beta_esd ?
_cell.angle_gamma 110.506
_cell.angle_gamma_esd ?
_cell.entry_id 8T89
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 11.690
_cell.length_a_esd ?
_cell.length_b 11.700
_cell.length_b_esd ?
_cell.length_c 18.510
_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 8T89
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 2
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P -1'
_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 'Racemic mixture of amyloid beta segment 16-KLVFFA-21' 724.909 1 ? ? ? ?
2 non-polymer syn 'trifluoroacetic acid' 114.023 1 ? ? ? ?
3 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 no
_entity_poly.pdbx_seq_one_letter_code KLVFFA
_entity_poly.pdbx_seq_one_letter_code_can KLVFFA
_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 LYS n
1 2 LEU n
1 3 VAL n
1 4 PHE n
1 5 PHE n
1 6 ALA 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 6
_pdbx_entity_src_syn.organism_scientific 'Homo sapiens'
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 9606
_pdbx_entity_src_syn.details ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 8T89
_struct_ref.pdbx_db_accession 8T89
_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 8T89
_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 6
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 8T89
_struct_ref_seq.db_align_beg 16
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 21
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 16
_struct_ref_seq.pdbx_auth_seq_align_end 21
#
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
HOH non-polymer . WATER ? 'H2 O' 18.015
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
TFA non-polymer . 'trifluoroacetic acid' ? 'C2 H F3 O2' 114.023
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146
#
_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 8T89
_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 1.63
_exptl_crystal.density_method ?
_exptl_crystal.density_percent_sol 24.76
_exptl_crystal.description needle-shaped
_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 'BATCH MODE'
_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 'hexafluoroisopropanol, water'
_exptl_crystal_grow.pdbx_pH_range ?
_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 16M'
_diffrn_detector.area_resol_mean ?
_diffrn_detector.dtime ?
_diffrn_detector.pdbx_frames_total ?
_diffrn_detector.pdbx_collection_time_total ?
_diffrn_detector.pdbx_collection_date 2023-03-31
_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 0.97918
_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 'APS BEAMLINE 24-ID-E'
_diffrn_source.voltage ?
_diffrn_source.take-off_angle ?
_diffrn_source.pdbx_wavelength_list 0.97918
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_synchrotron_beamline 24-ID-E
_diffrn_source.pdbx_synchrotron_site APS
#
_reflns.B_iso_Wilson_estimate ?
_reflns.entry_id 8T89
_reflns.data_reduction_details ?
_reflns.data_reduction_method ?
_reflns.d_resolution_high 1.5
_reflns.d_resolution_low 18.50
_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 1426
_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 97.0
_reflns.R_free_details ?
_reflns.Rmerge_F_all ?
_reflns.Rmerge_F_obs ?
_reflns.Friedel_coverage ?
_reflns.number_gt ?
_reflns.threshold_expression ?
_reflns.pdbx_redundancy 6.0
_reflns.pdbx_netI_over_av_sigmaI ?
_reflns.pdbx_netI_over_sigmaI 4.49
_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 0.172
_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 0.997
_reflns.pdbx_CC_star ?
_reflns.pdbx_R_split ?
_reflns.pdbx_Rmerge_I_obs 0.157
_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 ?
#
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_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
_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
_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
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_CC_half
_reflns_shell.pdbx_CC_star
_reflns_shell.pdbx_R_split
_reflns_shell.percent_possible_all
_reflns_shell.Rmerge_I_all
_reflns_shell.Rmerge_I_obs
_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
1.50 1.56 ? ? ? ? ? ? 139 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1.265 ? ? 1 1 0.767 ? ? ? ? 1.159 ? ? ? ? ? ? ? ? ?
1.56 1.62 ? ? ? ? ? ? 146 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1.067 ? ? 2 1 0.841 ? ? ? ? 0.979 ? ? ? ? ? ? ? ? ?
1.62 1.69 ? ? ? ? ? ? 149 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.83 ? ? 3 1 0.907 ? ? ? ? 0.761 ? ? ? ? ? ? ? ? ?
1.69 1.77 ? ? ? ? ? ? 122 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.613 ? ? 4 1 0.933 ? ? ? ? 0.561 ? ? ? ? ? ? ? ? ?
1.77 1.87 ? ? ? ? ? ? 128 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.403 ? ? 5 1 0.981 ? ? ? ? 0.369 ? ? ? ? ? ? ? ? ?
1.87 1.98 ? ? ? ? ? ? 120 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.356 ? ? 6 1 0.976 ? ? ? ? 0.323 ? ? ? ? ? ? ? ? ?
1.98 2.12 ? ? ? ? ? ? 103 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.246 ? ? 7 1 0.983 ? ? ? ? 0.224 ? ? ? ? ? ? ? ? ?
2.12 2.29 ? ? ? ? ? ? 115 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.233 ? ? 8 1 0.994 ? ? ? ? 0.214 ? ? ? ? ? ? ? ? ?
2.29 2.51 ? ? ? ? ? ? 92 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.231 ? ? 9 1 0.973 ? ? ? ? 0.209 ? ? ? ? ? ? ? ? ?
2.51 2.81 ? ? ? ? ? ? 91 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.178 ? ? 10 1 0.993 ? ? ? ? 0.161 ? ? ? ? ? ? ? ? ?
2.81 3.24 ? ? ? ? ? ? 79 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.149 ? ? 11 1 0.995 ? ? ? ? 0.136 ? ? ? ? ? ? ? ? ?
3.24 3.97 ? ? ? ? ? ? 63 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.132 ? ? 12 1 0.991 ? ? ? ? 0.119 ? ? ? ? ? ? ? ? ?
3.97 5.61 ? ? ? ? ? ? 54 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.094 ? ? 13 1 0.998 ? ? ? ? 0.086 ? ? ? ? ? ? ? ? ?
5.61 18.50 ? ? ? ? ? ? 23 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.154 ? ? 14 1 0.997 ? ? ? ? 0.141 ? ? ? ? ? ? ? ? ?
#
_refine.aniso_B[1][1] -0.834
_refine.aniso_B[1][2] 1.272
_refine.aniso_B[1][3] 0.288
_refine.aniso_B[2][2] 1.116
_refine.aniso_B[2][3] -0.319
_refine.aniso_B[3][3] -1.546
_refine.B_iso_max ?
_refine.B_iso_mean 24.810
_refine.B_iso_min ?
_refine.correlation_coeff_Fo_to_Fc 0.976
_refine.correlation_coeff_Fo_to_Fc_free 0.970
_refine.details 'Hydrogens have been used if present in the input file'
_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 8T89
_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 1.500
_refine.ls_d_res_low 18.500
_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 1426
_refine.ls_number_reflns_R_free 143
_refine.ls_number_reflns_R_work 1283
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 97.007
_refine.ls_percent_reflns_R_free 10.028
_refine.ls_R_factor_all 0.225
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_R_free 0.2270
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work 0.2252
_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 'AB INITIO PHASING'
_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 0.086
_refine.pdbx_overall_ESU_R_Free 0.078
_refine.pdbx_solvent_vdw_probe_radii 1.200
_refine.pdbx_solvent_ion_probe_radii 0.800
_refine.pdbx_solvent_shrinkage_radii 0.800
_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 ?
_refine.overall_SU_ML ?
_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.pdbx_number_atoms_protein 52
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 7
_refine_hist.number_atoms_solvent 2
_refine_hist.number_atoms_total 61
_refine_hist.d_res_high 1.500
_refine_hist.d_res_low 18.500
#
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' ? 0.012 0.012 59 ? r_bond_refined_d ? ?
'X-RAY DIFFRACTION' ? 0.030 0.016 57 ? r_bond_other_d ? ?
'X-RAY DIFFRACTION' ? 1.577 1.589 79 ? r_angle_refined_deg ? ?
'X-RAY DIFFRACTION' ? 0.511 1.566 128 ? r_angle_other_deg ? ?
'X-RAY DIFFRACTION' ? 5.502 5.000 5 ? r_dihedral_angle_1_deg ? ?
'X-RAY DIFFRACTION' ? 16.043 10.000 9 ? r_dihedral_angle_3_deg ? ?
'X-RAY DIFFRACTION' ? 14.756 10.000 2 ? r_dihedral_angle_6_deg ? ?
'X-RAY DIFFRACTION' ? 0.058 0.200 9 ? r_chiral_restr ? ?
'X-RAY DIFFRACTION' ? 0.010 0.020 57 ? r_gen_planes_refined ? ?
'X-RAY DIFFRACTION' ? 0.000 0.020 15 ? r_gen_planes_other ? ?
'X-RAY DIFFRACTION' ? 0.134 0.200 2 ? r_nbd_refined ? ?
'X-RAY DIFFRACTION' ? 0.163 0.200 34 ? r_symmetry_nbd_other ? ?
'X-RAY DIFFRACTION' ? 0.212 0.200 24 ? r_nbtor_refined ? ?
'X-RAY DIFFRACTION' ? 0.094 0.200 34 ? r_symmetry_nbtor_other ? ?
'X-RAY DIFFRACTION' ? 0.031 0.200 2 ? r_xyhbond_nbd_refined ? ?
'X-RAY DIFFRACTION' ? 0.135 0.200 3 ? r_symmetry_nbd_refined ? ?
'X-RAY DIFFRACTION' ? 0.139 0.200 32 ? r_nbd_other ? ?
'X-RAY DIFFRACTION' ? 0.120 0.200 4 ? r_symmetry_xyhbond_nbd_refined ? ?
'X-RAY DIFFRACTION' ? 2.100 1.890 23 ? r_mcbond_it ? ?
'X-RAY DIFFRACTION' ? 2.106 1.860 23 ? r_mcbond_other ? ?
'X-RAY DIFFRACTION' ? 3.266 2.772 27 ? r_mcangle_it ? ?
'X-RAY DIFFRACTION' ? 3.385 2.819 28 ? r_mcangle_other ? ?
'X-RAY DIFFRACTION' ? 4.535 2.740 36 ? r_scbond_it ? ?
'X-RAY DIFFRACTION' ? 3.911 2.449 31 ? r_scbond_other ? ?
'X-RAY DIFFRACTION' ? 6.718 3.928 52 ? r_scangle_it ? ?
'X-RAY DIFFRACTION' ? 5.827 3.459 44 ? r_scangle_other ? ?
'X-RAY DIFFRACTION' ? 8.269 42.362 51 ? r_lrange_it ? ?
'X-RAY DIFFRACTION' ? 8.037 35.129 49 ? r_lrange_other ? ?
#
loop_
_refine_ls_shell.pdbx_refine_id
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.percent_reflns_obs
_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
_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
_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
'X-RAY DIFFRACTION' 1.500 1.676 431 . 42 375 96.7517 . 0.361 . . 0.363 . . . . . 0.333 . 5 . 0.879 0.846 0.340
'X-RAY DIFFRACTION' 1.676 1.932 359 . 35 313 96.9359 . 0.269 . . 0.268 . . . . . 0.234 . 5 . 0.932 0.915 0.281
'X-RAY DIFFRACTION' 1.932 2.360 305 . 29 264 96.0656 . 0.235 . . 0.239 . . . . . 0.231 . 5 . 0.960 0.971 0.210
'X-RAY DIFFRACTION' 2.360 3.311 238 . 23 212 98.7395 . 0.209 . . 0.209 . . . . . 0.219 . 5 . 0.978 0.981 0.212
'X-RAY DIFFRACTION' 3.311 18.500 137 . 14 119 97.0803 . 0.168 . . 0.165 . . . . . 0.248 . 5 . 0.988 0.985 0.199
#
_struct.entry_id 8T89
_struct.title 'Racemic mixture of amyloid beta segment 16-KLVFFA-21 forms heterochiral rippled beta-sheet'
_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 8T89
_struct_keywords.text 'Rippled beta sheet, amyloid fibril, 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 ?
C N N 3 ?
#
_atom_sites.entry_id 8T89
_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.fract_transf_matrix[1][1] 0.085543
_atom_sites.fract_transf_matrix[1][2] 0.031994
_atom_sites.fract_transf_matrix[1][3] 0.003000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.091252
_atom_sites.fract_transf_matrix[2][3] 0.000983
_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] 0.054054
_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
_atom_type.scat_Cromer_Mann_c
C 6 6 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 0.216
F 9 9 3.539 10.282 2.641 4.294 1.517 0.262 1.024 26.148 0.304
H 1 1 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800 0.003
N 7 7 12.222 0.006 3.135 9.893 2.014 28.997 1.167 0.583 -11.538
O 8 8 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 0.251
#
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
ATOM 1 N N . LYS A 1 1 ? -5.348 6.055 16.461 1.000 19.660 0 16 LYS A N 1 ?
ATOM 2 C CA . LYS A 1 1 ? -4.123 5.550 15.848 1.000 17.920 0 16 LYS A CA 1 ?
ATOM 3 C C . LYS A 1 1 ? -3.894 6.204 14.496 1.000 17.290 0 16 LYS A C 1 ?
ATOM 4 O O . LYS A 1 1 ? -4.854 6.505 13.796 1.000 19.840 0 16 LYS A O 1 ?
ATOM 5 C CB . LYS A 1 1 ? -4.300 4.042 15.642 1.000 21.380 0 16 LYS A CB 1 ?
ATOM 6 C CG . LYS A 1 1 ? -3.030 3.257 15.899 1.000 29.530 0 16 LYS A CG 1 ?
ATOM 7 C CD . LYS A 1 1 ? -2.785 3.108 17.407 1.000 32.110 0 16 LYS A CD 1 ?
ATOM 8 C CE . LYS A 1 1 ? -3.669 2.037 18.008 1.000 40.740 0 16 LYS A CE 1 ?
ATOM 9 N NZ . LYS A 1 1 ? -3.520 1.999 19.487 1.000 41.570 0 16 LYS A NZ 1 ?
ATOM 10 H H2 . LYS A 1 1 ? -5.125 6.654 17.178 1.000 19.130 0 16 LYS A H2 1 c
ATOM 11 H H3 . LYS A 1 1 ? -5.883 6.516 15.811 1.000 19.110 0 16 LYS A H3 1 c
ATOM 12 H HA . LYS A 1 1 ? -3.359 5.726 16.443 1.000 18.790 0 16 LYS A HA 1 c
ATOM 13 H HB2 . LYS A 1 1 ? -5.002 3.721 16.244 1.000 22.210 0 16 LYS A HB2 1 c
ATOM 14 H HB3 . LYS A 1 1 ? -4.592 3.879 14.721 1.000 22.140 0 16 LYS A HB3 1 c
ATOM 15 H HG2 . LYS A 1 1 ? -3.106 2.370 15.490 1.000 27.900 0 16 LYS A HG2 1 c
ATOM 16 H HG3 . LYS A 1 1 ? -2.271 3.724 15.488 1.000 27.900 0 16 LYS A HG3 1 c
ATOM 17 H HD2 . LYS A 1 1 ? -1.845 2.874 17.562 1.000 33.290 0 16 LYS A HD2 1 c
ATOM 18 H HD3 . LYS A 1 1 ? -2.964 3.962 17.853 1.000 33.210 0 16 LYS A HD3 1 c
ATOM 19 H HE2 . LYS A 1 1 ? -4.602 2.214 17.786 1.000 38.590 0 16 LYS A HE2 1 c
ATOM 20 H HE3 . LYS A 1 1 ? -3.429 1.166 17.639 1.000 38.670 0 16 LYS A HE3 1 c
ATOM 21 H HZ1 . LYS A 1 1 ? -4.295 1.719 19.866 1.000 41.300 0 16 LYS A HZ1 1 c
ATOM 22 H HZ2 . LYS A 1 1 ? -2.857 1.425 19.713 1.000 41.300 0 16 LYS A HZ2 1 c
ATOM 23 H HZ3 . LYS A 1 1 ? -3.318 2.825 19.801 1.000 41.260 0 16 LYS A HZ3 1 c
ATOM 24 N N . LEU A 1 2 ? -2.637 6.324 14.099 1.000 16.950 0 17 LEU A N 1 ?
ATOM 25 C CA . LEU A 1 2 ? -2.306 6.891 12.801 1.000 16.380 0 17 LEU A CA 1 ?
ATOM 26 C C . LEU A 1 2 ? -1.060 6.175 12.322 1.000 17.650 0 17 LEU A C 1 ?
ATOM 27 O O . LEU A 1 2 ? -0.036 6.204 13.004 1.000 18.790 0 17 LEU A O 1 ?
ATOM 28 C CB . LEU A 1 2 ? -2.057 8.388 12.994 1.000 21.190 0 17 LEU A CB 1 ?
ATOM 29 C CG . LEU A 1 2 ? -1.803 9.204 11.746 1.000 24.700 0 17 LEU A CG 1 ?
ATOM 30 C CD1 . LEU A 1 2 ? -3.051 9.362 10.951 1.000 26.730 0 17 LEU A CD1 1 ?
ATOM 31 C CD2 . LEU A 1 2 ? -1.317 10.604 12.144 1.000 31.320 0 17 LEU A CD2 1 ?
ATOM 32 H H . LEU A 1 2 ? -1.889 6.018 14.706 1.000 16.900 0 17 LEU A H 1 c
ATOM 33 H HA . LEU A 1 2 ? -3.047 6.741 12.173 1.000 17.590 0 17 LEU A HA 1 c
ATOM 34 H HB2 . LEU A 1 2 ? -2.832 8.767 13.454 1.000 20.700 0 17 LEU A HB2 1 c
ATOM 35 H HB3 . LEU A 1 2 ? -1.287 8.492 13.588 1.000 20.690 0 17 LEU A HB3 1 c
ATOM 36 H HG . LEU A 1 2 ? -1.114 8.760 11.193 1.000 25.470 0 17 LEU A HG 1 c
ATOM 37 H HD11 . LEU A 1 2 ? -2.877 9.935 10.184 1.000 26.090 0 17 LEU A HD11 1 c
ATOM 38 H HD12 . LEU A 1 2 ? -3.351 8.491 10.642 1.000 26.040 0 17 LEU A HD12 1 c
ATOM 39 H HD13 . LEU A 1 2 ? -3.741 9.766 11.506 1.000 26.070 0 17 LEU A HD13 1 c
ATOM 40 H HD21 . LEU A 1 2 ? -1.251 11.164 11.351 1.000 29.100 0 17 LEU A HD21 1 c
ATOM 41 H HD22 . LEU A 1 2 ? -1.947 11.001 12.770 1.000 29.110 0 17 LEU A HD22 1 c
ATOM 42 H HD23 . LEU A 1 2 ? -0.442 10.534 12.564 1.000 29.110 0 17 LEU A HD23 1 c
ATOM 43 N N . VAL A 1 3 ? -1.186 5.495 11.190 1.000 16.670 0 18 VAL A N 1 ?
ATOM 44 C CA . VAL A 1 3 ? -0.097 4.751 10.603 1.000 16.980 0 18 VAL A CA 1 ?
ATOM 45 C C . VAL A 1 3 ? 0.080 5.221 9.171 1.000 17.990 0 18 VAL A C 1 ?
ATOM 46 O O . VAL A 1 3 ? -0.900 5.289 8.433 1.000 18.830 0 18 VAL A O 1 ?
ATOM 47 C CB . VAL A 1 3 ? -0.407 3.245 10.662 1.000 19.120 0 18 VAL A CB 1 ?
ATOM 48 C CG1 . VAL A 1 3 ? 0.678 2.450 9.968 1.000 22.640 0 18 VAL A CG1 1 ?
ATOM 49 C CG2 . VAL A 1 3 ? -0.565 2.771 12.094 1.000 20.810 0 18 VAL A CG2 1 ?
ATOM 50 H H . VAL A 1 3 ? -2.077 5.494 10.715 1.000 16.970 0 18 VAL A H 1 c
ATOM 51 H HA . VAL A 1 3 ? 0.717 4.929 11.102 1.000 17.500 0 18 VAL A HA 1 c
ATOM 52 H HB . VAL A 1 3 ? -1.260 3.089 10.186 1.000 19.610 0 18 VAL A HB 1 c
ATOM 53 H HG11 . VAL A 1 3 ? 0.590 1.509 10.198 1.000 21.480 0 18 VAL A HG11 1 c
ATOM 54 H HG12 . VAL A 1 3 ? 0.596 2.554 9.004 1.000 21.480 0 18 VAL A HG12 1 c
ATOM 55 H HG13 . VAL A 1 3 ? 1.550 2.773 10.254 1.000 21.480 0 18 VAL A HG13 1 c
ATOM 56 H HG21 . VAL A 1 3 ? -0.656 1.802 12.109 1.000 20.270 0 18 VAL A HG21 1 c
ATOM 57 H HG22 . VAL A 1 3 ? 0.217 3.030 12.610 1.000 20.270 0 18 VAL A HG22 1 c
ATOM 58 H HG23 . VAL A 1 3 ? -1.359 3.175 12.485 1.000 20.260 0 18 VAL A HG23 1 c
ATOM 59 N N . PHE A 1 4 ? 1.301 5.492 8.755 1.000 16.490 0 19 PHE A N 1 ?
ATOM 60 C CA . PHE A 1 4 ? 1.538 6.094 7.454 1.000 16.950 0 19 PHE A CA 1 ?
ATOM 61 C C . PHE A 1 4 ? 2.820 5.516 6.881 1.000 17.350 0 19 PHE A C 1 ?
ATOM 62 O O . PHE A 1 4 ? 3.859 5.581 7.541 1.000 18.300 0 19 PHE A O 1 ?
ATOM 63 C CB . PHE A 1 4 ? 1.656 7.623 7.586 1.000 19.180 0 19 PHE A CB 1 ?
ATOM 64 C CG . PHE A 1 4 ? 1.576 8.368 6.279 1.000 22.130 0 19 PHE A CG 1 ?
ATOM 65 C CD1 . PHE A 1 4 ? 2.664 8.440 5.435 1.000 29.760 0 19 PHE A CD1 1 ?
ATOM 66 C CD2 . PHE A 1 4 ? 0.365 8.921 5.876 1.000 26.630 0 19 PHE A CD2 1 ?
ATOM 67 C CE1 . PHE A 1 4 ? 2.556 9.117 4.227 1.000 33.890 0 19 PHE A CE1 1 ?
ATOM 68 C CE2 . PHE A 1 4 ? 0.247 9.584 4.661 1.000 30.720 0 19 PHE A CE2 1 ?
ATOM 69 C CZ . PHE A 1 4 ? 1.354 9.679 3.850 1.000 32.280 0 19 PHE A CZ 1 ?
ATOM 70 H H . PHE A 1 4 ? 2.091 5.278 9.347 1.000 16.940 0 19 PHE A H 1 c
ATOM 71 H HA . PHE A 1 4 ? 0.786 5.876 6.848 1.000 17.340 0 19 PHE A HA 1 c
ATOM 72 H HB2 . PHE A 1 4 ? 0.939 7.939 8.174 1.000 19.290 0 19 PHE A HB2 1 c
ATOM 73 H HB3 . PHE A 1 4 ? 2.511 7.833 8.017 1.000 19.270 0 19 PHE A HB3 1 c
ATOM 74 H HD1 . PHE A 1 4 ? 3.489 8.063 5.696 1.000 28.550 0 19 PHE A HD1 1 c
ATOM 75 H HD2 . PHE A 1 4 ? -0.386 8.853 6.444 1.000 26.560 0 19 PHE A HD2 1 c
ATOM 76 H HE1 . PHE A 1 4 ? 3.307 9.183 3.658 1.000 31.970 0 19 PHE A HE1 1 c
ATOM 77 H HE2 . PHE A 1 4 ? -0.573 9.976 4.406 1.000 29.840 0 19 PHE A HE2 1 c
ATOM 78 H HZ . PHE A 1 4 ? 1.289 10.130 3.024 1.000 31.770 0 19 PHE A HZ 1 c
ATOM 79 N N . PHE A 1 5 ? 2.721 4.896 5.705 1.000 16.860 0 20 PHE A N 1 ?
ATOM 80 C CA . PHE A 1 5 ? 3.857 4.350 5.002 1.000 15.450 0 20 PHE A CA 1 ?
ATOM 81 C C . PHE A 1 5 ? 4.072 5.147 3.725 1.000 20.250 0 20 PHE A C 1 ?
ATOM 82 O O . PHE A 1 5 ? 3.139 5.537 3.026 1.000 21.640 0 20 PHE A O 1 ?
ATOM 83 C CB . PHE A 1 5 ? 3.652 2.861 4.685 1.000 16.560 0 20 PHE A CB 1 ?
ATOM 84 C CG . PHE A 1 5 ? 3.578 2.030 5.922 1.000 18.730 0 20 PHE A CG 1 ?
ATOM 85 C CD1 . PHE A 1 5 ? 4.704 1.856 6.687 1.000 20.180 0 20 PHE A CD1 1 ?
ATOM 86 C CD2 . PHE A 1 5 ? 2.408 1.459 6.340 1.000 21.820 0 20 PHE A CD2 1 ?
ATOM 87 C CE1 . PHE A 1 5 ? 4.672 1.094 7.836 1.000 20.360 0 20 PHE A CE1 1 ?
ATOM 88 C CE2 . PHE A 1 5 ? 2.387 0.682 7.492 1.000 24.230 0 20 PHE A CE2 1 ?
ATOM 89 C CZ . PHE A 1 5 ? 3.512 0.536 8.255 1.000 23.420 0 20 PHE A CZ 1 ?
ATOM 90 H H . PHE A 1 5 ? 1.809 4.799 5.282 1.000 16.630 0 20 PHE A H 1 c
ATOM 91 H HA . PHE A 1 5 ? 4.659 4.445 5.572 1.000 16.790 0 20 PHE A HA 1 c
ATOM 92 H HB2 . PHE A 1 5 ? 2.823 2.756 4.173 1.000 16.790 0 20 PHE A HB2 1 c
ATOM 93 H HB3 . PHE A 1 5 ? 4.397 2.549 4.130 1.000 16.780 0 20 PHE A HB3 1 c
ATOM 94 H HD1 . PHE A 1 5 ? 5.515 2.253 6.413 1.000 20.010 0 20 PHE A HD1 1 c
ATOM 95 H HD2 . PHE A 1 5 ? 1.623 1.564 5.826 1.000 21.500 0 20 PHE A HD2 1 c
ATOM 96 H HE1 . PHE A 1 5 ? 5.456 0.988 8.350 1.000 21.000 0 20 PHE A HE1 1 c
ATOM 97 H HE2 . PHE A 1 5 ? 1.576 0.293 7.778 1.000 23.160 0 20 PHE A HE2 1 c
ATOM 98 H HZ . PHE A 1 5 ? 3.493 0.007 9.036 1.000 22.620 0 20 PHE A HZ 1 c
ATOM 99 N N . ALA A 1 6 ? 5.337 5.296 3.368 1.000 21.190 0 21 ALA A N 1 ?
ATOM 100 C CA . ALA A 1 6 ? 5.700 5.860 2.073 1.000 23.280 0 21 ALA A CA 1 ?
ATOM 101 C C . ALA A 1 6 ? 6.898 5.102 1.486 1.000 30.240 0 21 ALA A C 1 ?
ATOM 102 O O . ALA A 1 6 ? 7.031 5.023 0.254 1.000 31.220 0 21 ALA A O 1 ?
ATOM 103 C CB . ALA A 1 6 ? 6.026 7.301 2.262 1.000 25.850 0 21 ALA A CB 1 ?
ATOM 104 O OXT . ALA A 1 6 ? 7.736 4.547 2.229 1.000 23.990 0 21 ALA A OXT 1 ?
ATOM 105 H H . ALA A 1 6 ? 6.073 5.016 4.000 1.000 21.420 0 21 ALA A H 1 c
ATOM 106 H HA . ALA A 1 6 ? 4.936 5.776 1.455 1.000 24.510 0 21 ALA A HA 1 c
ATOM 107 H HB1 . ALA A 1 6 ? 6.235 7.703 1.401 1.000 25.030 0 21 ALA A HB1 1 c
ATOM 108 H HB2 . ALA A 1 6 ? 5.263 7.758 2.655 1.000 25.030 0 21 ALA A HB2 1 c
ATOM 109 H HB3 . ALA A 1 6 ? 6.793 7.388 2.852 1.000 25.030 0 21 ALA A HB3 1 c
HETATM 110 C C1 . TFA B 2 . ? -5.141 9.471 16.454 1.000 35.750 0 101 TFA A C1 1 ?
HETATM 111 C C2 . TFA B 2 . ? -4.525 10.839 16.162 1.000 48.930 0 101 TFA A C2 1 ?
HETATM 112 O O . TFA B 2 . ? -6.405 9.444 16.514 1.000 38.980 0 101 TFA A O 1 ?
HETATM 113 F F1 . TFA B 2 . ? -4.835 11.658 17.128 1.000 45.990 0 101 TFA A F1 1 ?
HETATM 114 F F2 . TFA B 2 . ? -3.181 10.870 16.089 1.000 45.760 0 101 TFA A F2 1 ?
HETATM 115 F F3 . TFA B 2 . ? -4.969 11.337 15.031 1.000 44.060 0 101 TFA A F3 1 ?
HETATM 116 O OXT . TFA B 2 . ? -4.331 8.599 16.702 1.000 29.400 0 101 TFA A OXT 1 ?
HETATM 117 O O . HOH C 3 . ? 2.805 7.442 0.881 1.000 33.160 0 201 HOH A O 1 ?
HETATM 118 O O A HOH C 3 . ? -5.459 -0.383 19.354 0.500 27.360 0 202 HOH A O 1 ?
HETATM 119 O O B HOH C 3 . ? -8.704 9.220 17.913 0.500 28.490 0 202 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 LYS 1 16 16 LYS LYS A . n
A 1 2 LEU 2 17 17 LEU LEU A . n
A 1 3 VAL 3 18 18 VAL VAL A . n
A 1 4 PHE 4 19 19 PHE PHE A . n
A 1 5 PHE 5 20 20 PHE PHE A . n
A 1 6 ALA 6 21 21 ALA ALA A . n
#
_pdbx_contact_author.id 2
_pdbx_contact_author.email jraskato@ucsc.edu
_pdbx_contact_author.name_first Jevgenij
_pdbx_contact_author.name_last Raskatov
_pdbx_contact_author.name_mi A
_pdbx_contact_author.role 'principal investigator/group leader'
_pdbx_contact_author.identifier_ORCID 0000-0002-0082-9113
#
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 TFA 1 101 101 TFA TFA A .
C 3 HOH 1 201 102 HOH HOH A .
C 3 HOH 2 202 103 HOH HOH A .
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_defined_assembly
_pdbx_struct_assembly.method_details ?
_pdbx_struct_assembly.oligomeric_details hexameric
_pdbx_struct_assembly.oligomeric_count 6
#
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_assembly_gen.asym_id_list
1 1 A,B,C
1 2 A,B,C
1 3 A,B,C
1 4 A,B,C
1 5 A,B,C
1 6 A,B,C
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
2 'crystal symmetry operation' 1_655 x+1,y,z 1.0000000000 0.0000000000 0.0000000000 11.6900000000 0.0000000000
1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
3 'crystal symmetry operation' 1_455 x-1,y,z 1.0000000000 0.0000000000 0.0000000000 -11.6900000000 0.0000000000
1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
4 'crystal symmetry operation' 2_566 -x,-y+1,-z+1 -1.0000000000 0.0000000000 0.0000000000 -4.6728832539 0.0000000000
-1.0000000000 0.0000000000 10.7593626905 0.0000000000 0.0000000000 -1.0000000000 18.5000151136
5 'crystal symmetry operation' 2_466 -x-1,-y+1,-z+1 -1.0000000000 0.0000000000 0.0000000000 -16.3628832539 0.0000000000
-1.0000000000 0.0000000000 10.7593626905 0.0000000000 0.0000000000 -1.0000000000 18.5000151136
6 'crystal symmetry operation' 2_666 -x+1,-y+1,-z+1 -1.0000000000 0.0000000000 0.0000000000 7.0171167461 0.0000000000
-1.0000000000 0.0000000000 10.7593626905 0.0000000000 0.0000000000 -1.0000000000 18.5000151136
#
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 2023-11-29
2 'Structure model' 1 1 2023-12-13
#
_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 'Database references'
#
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
#
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_volume'
2 2 'Structure model' '_citation.page_first'
3 2 'Structure model' '_citation.page_last'
4 2 'Structure model' '_citation_author.identifier_ORCID'
#
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 ? ? ? 5.8.0352 1
? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2
? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3
? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXT ? ? ? . 4
#
_pdbx_entry_details.entry_id 8T89
_pdbx_entry_details.has_ligand_of_interest N
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
#
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
HOH O O N N 14
HOH H1 H N N 15
HOH H2 H N N 16
LEU N N N N 17
LEU CA C N S 18
LEU C C N N 19
LEU O O N N 20
LEU CB C N N 21
LEU CG C N N 22
LEU CD1 C N N 23
LEU CD2 C N N 24
LEU OXT O N N 25
LEU H H N N 26
LEU H2 H N N 27
LEU HA H N N 28
LEU HB2 H N N 29
LEU HB3 H N N 30
LEU HG H N N 31
LEU HD11 H N N 32
LEU HD12 H N N 33
LEU HD13 H N N 34
LEU HD21 H N N 35
LEU HD22 H N N 36
LEU HD23 H N N 37
LEU HXT H N N 38
LYS N N N N 39
LYS CA C N S 40
LYS C C N N 41
LYS O O N N 42
LYS CB C N N 43
LYS CG C N N 44
LYS CD C N N 45
LYS CE C N N 46
LYS NZ N N N 47
LYS OXT O N N 48
LYS H H N N 49
LYS H2 H N N 50
LYS HA H N N 51
LYS HB2 H N N 52
LYS HB3 H N N 53
LYS HG2 H N N 54
LYS HG3 H N N 55
LYS HD2 H N N 56
LYS HD3 H N N 57
LYS HE2 H N N 58
LYS HE3 H N N 59
LYS HZ1 H N N 60
LYS HZ2 H N N 61
LYS HZ3 H N N 62
LYS HXT H N N 63
PHE N N N N 64
PHE CA C N S 65
PHE C C N N 66
PHE O O N N 67
PHE CB C N N 68
PHE CG C Y N 69
PHE CD1 C Y N 70
PHE CD2 C Y N 71
PHE CE1 C Y N 72
PHE CE2 C Y N 73
PHE CZ C Y N 74
PHE OXT O N N 75
PHE H H N N 76
PHE H2 H N N 77
PHE HA H N N 78
PHE HB2 H N N 79
PHE HB3 H N N 80
PHE HD1 H N N 81
PHE HD2 H N N 82
PHE HE1 H N N 83
PHE HE2 H N N 84
PHE HZ H N N 85
PHE HXT H N N 86
TFA C1 C N N 87
TFA C2 C N N 88
TFA O O N N 89
TFA F1 F N N 90
TFA F2 F N N 91
TFA F3 F N N 92
TFA OXT O N N 93
TFA HXT H N N 94
VAL N N N N 95
VAL CA C N S 96
VAL C C N N 97
VAL O O N N 98
VAL CB C N N 99
VAL CG1 C N N 100
VAL CG2 C N N 101
VAL OXT O N N 102
VAL H H N N 103
VAL H2 H N N 104
VAL HA H N N 105
VAL HB H N N 106
VAL HG11 H N N 107
VAL HG12 H N N 108
VAL HG13 H N N 109
VAL HG21 H N N 110
VAL HG22 H N N 111
VAL HG23 H N N 112
VAL HXT H N N 113
#
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
HOH O H1 sing N N 13
HOH O H2 sing N N 14
LEU N CA sing N N 15
LEU N H sing N N 16
LEU N H2 sing N N 17
LEU CA C sing N N 18
LEU CA CB sing N N 19
LEU CA HA sing N N 20
LEU C O doub N N 21
LEU C OXT sing N N 22
LEU CB CG sing N N 23
LEU CB HB2 sing N N 24
LEU CB HB3 sing N N 25
LEU CG CD1 sing N N 26
LEU CG CD2 sing N N 27
LEU CG HG sing N N 28
LEU CD1 HD11 sing N N 29
LEU CD1 HD12 sing N N 30
LEU CD1 HD13 sing N N 31
LEU CD2 HD21 sing N N 32
LEU CD2 HD22 sing N N 33
LEU CD2 HD23 sing N N 34
LEU OXT HXT sing N N 35
LYS N CA sing N N 36
LYS N H sing N N 37
LYS N H2 sing N N 38
LYS CA C sing N N 39
LYS CA CB sing N N 40
LYS CA HA sing N N 41
LYS C O doub N N 42
LYS C OXT sing N N 43
LYS CB CG sing N N 44
LYS CB HB2 sing N N 45
LYS CB HB3 sing N N 46
LYS CG CD sing N N 47
LYS CG HG2 sing N N 48
LYS CG HG3 sing N N 49
LYS CD CE sing N N 50
LYS CD HD2 sing N N 51
LYS CD HD3 sing N N 52
LYS CE NZ sing N N 53
LYS CE HE2 sing N N 54
LYS CE HE3 sing N N 55
LYS NZ HZ1 sing N N 56
LYS NZ HZ2 sing N N 57
LYS NZ HZ3 sing N N 58
LYS OXT HXT sing N N 59
PHE N CA sing N N 60
PHE N H sing N N 61
PHE N H2 sing N N 62
PHE CA C sing N N 63
PHE CA CB sing N N 64
PHE CA HA sing N N 65
PHE C O doub N N 66
PHE C OXT sing N N 67
PHE CB CG sing N N 68
PHE CB HB2 sing N N 69
PHE CB HB3 sing N N 70
PHE CG CD1 doub Y N 71
PHE CG CD2 sing Y N 72
PHE CD1 CE1 sing Y N 73
PHE CD1 HD1 sing N N 74
PHE CD2 CE2 doub Y N 75
PHE CD2 HD2 sing N N 76
PHE CE1 CZ doub Y N 77
PHE CE1 HE1 sing N N 78
PHE CE2 CZ sing Y N 79
PHE CE2 HE2 sing N N 80
PHE CZ HZ sing N N 81
PHE OXT HXT sing N N 82
TFA C1 C2 sing N N 83
TFA C1 O doub N N 84
TFA C1 OXT sing N N 85
TFA C2 F1 sing N N 86
TFA C2 F2 sing N N 87
TFA C2 F3 sing N N 88
TFA OXT HXT sing N N 89
VAL N CA sing N N 90
VAL N H sing N N 91
VAL N H2 sing N N 92
VAL CA C sing N N 93
VAL CA CB sing N N 94
VAL CA HA sing N N 95
VAL C O doub N N 96
VAL C OXT sing N N 97
VAL CB CG1 sing N N 98
VAL CB CG2 sing N N 99
VAL CB HB sing N N 100
VAL CG1 HG11 sing N N 101
VAL CG1 HG12 sing N N 102
VAL CG1 HG13 sing N N 103
VAL CG2 HG21 sing N N 104
VAL CG2 HG22 sing N N 105
VAL CG2 HG23 sing N N 106
VAL OXT HXT sing N N 107
#
_pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute on Aging (NIH/NIA)'
_pdbx_audit_support.country 'United States'
_pdbx_audit_support.grant_number AG074954
_pdbx_audit_support.ordinal 1
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 'trifluoroacetic acid' TFA
3 water HOH
#