data_5VOS # _entry.id 5VOS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 5VOS pdb_00005vos 10.2210/pdb5vos/pdb WWPDB D_1000227781 ? ? EMDB EMD-8720 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2018-01-03 2 'Structure model' 1 1 2018-01-10 3 'Structure model' 1 2 2018-03-07 4 'Structure model' 1 3 2018-04-25 5 'Structure model' 1 4 2018-06-06 6 'Structure model' 1 5 2019-11-20 7 'Structure model' 1 6 2021-06-30 8 'Structure model' 1 7 2024-03-13 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Refinement description' 6 6 'Structure model' 'Author supporting evidence' 7 7 'Structure model' 'Data collection' 8 8 'Structure model' 'Data collection' 9 8 'Structure model' '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 3 3 'Structure model' citation 4 4 'Structure model' diffrn_source 5 5 'Structure model' software 6 6 'Structure model' pdbx_audit_support 7 7 'Structure model' diffrn_detector 8 8 'Structure model' chem_comp_atom 9 8 'Structure model' chem_comp_bond 10 8 'Structure model' database_2 11 8 'Structure model' em_author_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_abbrev' 2 2 'Structure model' '_citation.pdbx_database_id_PubMed' 3 2 'Structure model' '_citation.title' 4 3 'Structure model' '_citation.journal_volume' 5 3 'Structure model' '_citation.page_first' 6 3 'Structure model' '_citation.page_last' 7 3 'Structure model' '_citation.title' 8 3 'Structure model' '_citation.year' 9 4 'Structure model' '_diffrn_source.source' 10 6 'Structure model' '_pdbx_audit_support.funding_organization' 11 7 'Structure model' '_diffrn_detector.detector' 12 8 'Structure model' '_database_2.pdbx_DOI' 13 8 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VOS _pdbx_database_status.recvd_initial_deposition_date 2017-05-03 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'homologous sequence from hIAPP' 5KNZ unspecified EMDB 'VGSNKGAIIGL from Amyloid Beta determined by MicroED' EMD-8720 'associated EM volume' # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Rodriguez, J.A.' 1 ? 'Sawaya, M.R.' 2 ? 'Cascio, D.' 3 ? 'Eisenberg, D.S.' 4 ? 'Griner, S.L.' 5 ? 'Gonen, T.' 6 ? # _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. Biol. Chem.' _citation.journal_id_ASTM JBCHA3 _citation.journal_id_CSD 0071 _citation.journal_id_ISSN 1083-351X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 293 _citation.language ? _citation.page_first 2888 _citation.page_last 2902 _citation.title ;Common fibrillar spines of amyloid-beta and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors. ; _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1074/jbc.M117.806109 _citation.pdbx_database_id_PubMed 29282295 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Krotee, P.' 1 ? primary 'Griner, S.L.' 2 ? primary 'Sawaya, M.R.' 3 ? primary 'Cascio, D.' 4 ? primary 'Rodriguez, J.A.' 5 ? primary 'Shi, D.' 6 ? primary 'Philipp, S.' 7 ? primary 'Murray, K.' 8 ? primary 'Saelices, L.' 9 ? primary 'Lee, J.' 10 ? primary 'Seidler, P.' 11 ? primary 'Glabe, C.G.' 12 ? primary 'Jiang, L.' 13 ? primary 'Gonen, T.' 14 ? primary 'Eisenberg, D.S.' 15 ? # 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 'Amyloid beta A4 protein' 1029.213 1 ? ? 'VGSNKGAIIGL peptide (residues 24-34, UNP residues 7-17)' ? 2 water nat water 18.015 1 ? ? ? ? # _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 VGSNKGAIIGL _entity_poly.pdbx_seq_one_letter_code_can VGSNKGAIIGL _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 VAL n 1 2 GLY n 1 3 SER n 1 4 ASN n 1 5 LYS n 1 6 GLY n 1 7 ALA n 1 8 ILE n 1 9 ILE n 1 10 GLY n 1 11 LEU 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 11 _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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 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 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 VAL 1 24 24 VAL VAL A . n A 1 2 GLY 2 25 25 GLY GLY A . n A 1 3 SER 3 26 26 SER SER A . n A 1 4 ASN 4 27 27 ASN ASN A . n A 1 5 LYS 5 28 28 LYS LYS A . n A 1 6 GLY 6 29 29 GLY GLY A . n A 1 7 ALA 7 30 30 ALA ALA A . n A 1 8 ILE 8 31 31 ILE ILE A . n A 1 9 ILE 9 32 32 ILE ILE A . n A 1 10 GLY 10 33 33 GLY GLY A . n A 1 11 LEU 11 34 34 LEU LEU A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id HOH _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id HOH _pdbx_nonpoly_scheme.auth_mon_id HOH _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 ? 'data scaling' ? ? 'Wolfgang Kabsch' ? ? ? ? ? ? http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? XSCALE ? ? package . 1 ? phasing ? ? 'Randy J. Read' cimr-phaser@lists.cam.ac.uk ? ? ? ? ? http://www-structmed.cimr.cam.ac.uk/phaser/ ? PHASER ? ? program . 2 ? refinement ? ? 'Garib N. Murshudov' garib@ysbl.york.ac.uk ? ? ? ? Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html ? REFMAC ? ? program . 3 ? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'July. 13, 2016' ? ? ? C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.22 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 100.020 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5VOS _cell.details ? _cell.formula_units_Z ? _cell.length_a 18.780 _cell.length_a_esd ? _cell.length_b 4.730 _cell.length_b_esd ? _cell.length_c 33.470 _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 ? # _symmetry.entry_id 5VOS _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 5VOS _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.42 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _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_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method Batch _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 4.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '50 mM sodium citrate, pH 4.0, 10% v/v DMSO' _exptl_crystal_grow.pdbx_pH_range ? # _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 ? # _diffrn_detector.details ? _diffrn_detector.detector CMOS _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'TVIPS F416 CMOS CAMERA' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-04-17 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.0251 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source 'ELECTRON MICROSCOPE' _diffrn_source.target ? _diffrn_source.type 'TECNAI F20 TEM' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.0251 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate 14.635 _reflns.entry_id 5VOS _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.420 _reflns.d_resolution_low 32.960 _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 1129 _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 -3.000 _reflns.percent_possible_obs 85.500 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.175 _reflns.pdbx_Rmerge_I_obs 0.222 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 4.880 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.926 _reflns.pdbx_scaling_rejects 33 _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 0.244 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 5843 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.980 _reflns.pdbx_R_split ? _reflns.pdbx_CC_star ? # 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_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _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_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split _reflns_shell.pdbx_CC_star 1.420 1.490 ? 1.090 ? 216 177 ? 84 47.500 ? ? ? ? 0.496 ? ? ? ? ? ? ? ? 2.571 ? ? ? ? 0.611 ? ? 1 1 0.452 ? ? 1.490 1.570 ? 3.100 ? 562 181 ? 136 75.100 ? ? ? ? 0.315 ? ? ? ? ? ? ? ? 4.132 ? ? ? ? 0.354 ? ? 2 1 0.899 ? ? 1.570 1.670 ? 2.240 ? 380 130 ? 106 81.500 ? ? ? ? 0.388 ? ? ? ? ? ? ? ? 3.585 ? ? ? ? 0.443 ? ? 3 1 0.855 ? ? 1.670 1.780 ? 2.660 ? 507 133 ? 115 86.500 ? ? ? ? 0.421 ? ? ? ? ? ? ? ? 4.409 ? ? ? ? 0.479 ? ? 4 1 0.654 ? ? 1.780 1.920 ? 3.740 ? 698 131 ? 127 96.900 ? ? ? ? 0.343 ? ? ? ? ? ? ? ? 5.496 ? ? ? ? 0.376 ? ? 5 1 0.977 ? ? 1.920 2.110 ? 5.830 ? 899 134 ? 133 99.300 ? ? ? ? 0.264 ? ? ? ? ? ? ? ? 6.759 ? ? ? ? 0.285 ? ? 6 1 0.977 ? ? 2.110 2.360 ? 6.640 ? 949 131 ? 129 98.500 ? ? ? ? 0.273 ? ? ? ? ? ? ? ? 7.357 ? ? ? ? 0.296 ? ? 7 1 0.942 ? ? 2.360 2.720 ? 6.200 ? 474 86 ? 86 100.000 ? ? ? ? 0.209 ? ? ? ? ? ? ? ? 5.512 ? ? ? ? 0.231 ? ? 8 1 0.990 ? ? 2.720 3.330 ? 7.020 ? 469 86 ? 86 100.000 ? ? ? ? 0.214 ? ? ? ? ? ? ? ? 5.453 ? ? ? ? 0.238 ? ? 9 1 0.922 ? ? 3.330 4.720 ? 10.090 ? 544 89 ? 88 98.900 ? ? ? ? 0.171 ? ? ? ? ? ? ? ? 6.182 ? ? ? ? 0.184 ? ? 10 1 0.976 ? ? 4.720 32.960 ? 8.340 ? 145 42 ? 39 92.900 ? ? ? ? 0.138 ? ? ? ? ? ? ? ? 3.718 ? ? ? ? 0.161 ? ? 11 1 0.989 ? ? # _refine.aniso_B[1][1] 1.0400 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 0.8300 _refine.aniso_B[2][2] -1.3000 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -0.0400 _refine.B_iso_max 42.180 _refine.B_iso_mean 13.1660 _refine.B_iso_min 4.420 _refine.correlation_coeff_Fo_to_Fc 0.9330 _refine.correlation_coeff_Fo_to_Fc_free 0.8810 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _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 5VOS _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.4200 _refine.ls_d_res_low 32.9600 _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 1014 _refine.ls_number_reflns_R_free 113 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 85.5100 _refine.ls_percent_reflns_R_free 10.0000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2389 _refine.ls_R_factor_R_free 0.2924 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2335 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1150 _refine.pdbx_overall_ESU_R_Free 0.1220 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _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 2.8710 _refine.overall_SU_ML 0.1000 _refine.overall_SU_R_Cruickshank_DPI 0.1152 _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.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.4200 _refine_hist.d_res_low 32.9600 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 73 _refine_hist.pdbx_number_residues_total 11 _refine_hist.pdbx_B_iso_mean_solvent 15.91 _refine_hist.pdbx_number_atoms_protein 72 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON CRYSTALLOGRAPHY' ? 0.016 0.019 71 ? r_bond_refined_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.003 0.020 81 ? r_bond_other_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.838 2.040 94 ? r_angle_refined_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.659 3.000 185 ? r_angle_other_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 8.714 5.000 10 ? r_dihedral_angle_1_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 52.256 30.000 1 ? r_dihedral_angle_2_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 15.734 15.000 13 ? r_dihedral_angle_3_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.076 0.200 12 ? r_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.005 0.020 80 ? r_gen_planes_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.000 0.020 12 ? r_gen_planes_other ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine_ls_shell.d_res_high 1.4220 _refine_ls_shell.d_res_low 1.4590 _refine_ls_shell.number_reflns_all 42 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 4 _refine_ls_shell.number_reflns_R_work 38 _refine_ls_shell.percent_reflns_obs 42.0000 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.4340 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.3670 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5VOS _struct.title 'VGSNKGAIIGL from Amyloid Beta determined by MicroED' _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 5VOS _struct_keywords.text 'Amyloid, steric zipper, 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 UNP _struct_ref.db_code L7XCZ9_HUMAN _struct_ref.pdbx_db_accession L7XCZ9 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code VGSNKGAIIGL _struct_ref.pdbx_align_begin 7 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5VOS _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 11 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession L7XCZ9 _struct_ref_seq.db_align_beg 7 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 24 _struct_ref_seq.pdbx_auth_seq_align_end 34 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B 1 2 A,B 1 3 A,B 1 4 A,B 1 5 A,B 1 6 A,B 1 7 A,B 1 8 A,B 1 9 A,B 1 10 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 ? # 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_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.7300000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9.4600000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_545 x,y-1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -4.7300000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 1_535 x,y-2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -9.4600000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 2_658 -x+1,y+1/2,-z+3 -1.0000000000 0.0000000000 0.0000000000 1.3094703251 0.0000000000 1.0000000000 0.0000000000 2.3650000000 0.0000000000 0.0000000000 -1.0000000000 98.8784541388 7 'crystal symmetry operation' 2_668 -x+1,y+3/2,-z+3 -1.0000000000 0.0000000000 0.0000000000 1.3094703251 0.0000000000 1.0000000000 0.0000000000 7.0950000000 0.0000000000 0.0000000000 -1.0000000000 98.8784541388 8 'crystal symmetry operation' 2_678 -x+1,y+5/2,-z+3 -1.0000000000 0.0000000000 0.0000000000 1.3094703251 0.0000000000 1.0000000000 0.0000000000 11.8250000000 0.0000000000 0.0000000000 -1.0000000000 98.8784541388 9 'crystal symmetry operation' 2_648 -x+1,y-1/2,-z+3 -1.0000000000 0.0000000000 0.0000000000 1.3094703251 0.0000000000 1.0000000000 0.0000000000 -2.3650000000 0.0000000000 0.0000000000 -1.0000000000 98.8784541388 10 'crystal symmetry operation' 2_638 -x+1,y-3/2,-z+3 -1.0000000000 0.0000000000 0.0000000000 1.3094703251 0.0000000000 1.0000000000 0.0000000000 -7.0950000000 0.0000000000 0.0000000000 -1.0000000000 98.8784541388 # _phasing.method MR # _em_3d_fitting.entry_id 5VOS _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol OTHER _em_3d_fitting.ref_space RECIPROCAL _em_3d_fitting.target_criteria 'Maximum likelihood' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 5VOS _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.resolution ? _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.symmetry_type '3D CRYSTAL' _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.euler_angles_details ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 4.0 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'Fibrils of Amyloid Beta segment 24-34' _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 5VOS _em_image_scans.id 1 _em_image_scans.dimension_height 2048 _em_image_scans.dimension_width 2048 _em_image_scans.frames_per_image ? _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image ? _em_image_scans.citation_id ? _em_image_scans.number_digital_images ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.details ? # _em_imaging.id 1 _em_imaging.entry_id 5VOS _em_imaging.accelerating_voltage 200 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TECNAI F20' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type Quantifoil _em_sample_support.method ? _em_sample_support.film_material ? _em_sample_support.citation_id ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 5VOS _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 5VOS _em_experiment.id 1 _em_experiment.aggregation_state '3D ARRAY' _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.entity_assembly_id 1 # 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 GLY N N N N 31 GLY CA C N N 32 GLY C C N N 33 GLY O O N N 34 GLY OXT O N N 35 GLY H H N N 36 GLY H2 H N N 37 GLY HA2 H N N 38 GLY HA3 H N N 39 GLY HXT H N N 40 HOH O O N N 41 HOH H1 H N N 42 HOH H2 H N N 43 ILE N N N N 44 ILE CA C N S 45 ILE C C N N 46 ILE O O N N 47 ILE CB C N S 48 ILE CG1 C N N 49 ILE CG2 C N N 50 ILE CD1 C N N 51 ILE OXT O N N 52 ILE H H N N 53 ILE H2 H N N 54 ILE HA H N N 55 ILE HB H N N 56 ILE HG12 H N N 57 ILE HG13 H N N 58 ILE HG21 H N N 59 ILE HG22 H N N 60 ILE HG23 H N N 61 ILE HD11 H N N 62 ILE HD12 H N N 63 ILE HD13 H N N 64 ILE HXT H N N 65 LEU N N N N 66 LEU CA C N S 67 LEU C C N N 68 LEU O O N N 69 LEU CB C N N 70 LEU CG C N N 71 LEU CD1 C N N 72 LEU CD2 C N N 73 LEU OXT O N N 74 LEU H H N N 75 LEU H2 H N N 76 LEU HA H N N 77 LEU HB2 H N N 78 LEU HB3 H N N 79 LEU HG H N N 80 LEU HD11 H N N 81 LEU HD12 H N N 82 LEU HD13 H N N 83 LEU HD21 H N N 84 LEU HD22 H N N 85 LEU HD23 H N N 86 LEU HXT H N N 87 LYS N N N N 88 LYS CA C N S 89 LYS C C N N 90 LYS O O N N 91 LYS CB C N N 92 LYS CG C N N 93 LYS CD C N N 94 LYS CE C N N 95 LYS NZ N N N 96 LYS OXT O N N 97 LYS H H N N 98 LYS H2 H N N 99 LYS HA H N N 100 LYS HB2 H N N 101 LYS HB3 H N N 102 LYS HG2 H N N 103 LYS HG3 H N N 104 LYS HD2 H N N 105 LYS HD3 H N N 106 LYS HE2 H N N 107 LYS HE3 H N N 108 LYS HZ1 H N N 109 LYS HZ2 H N N 110 LYS HZ3 H N N 111 LYS HXT H N N 112 SER N N N N 113 SER CA C N S 114 SER C C N N 115 SER O O N N 116 SER CB C N N 117 SER OG O N N 118 SER OXT O N N 119 SER H H N N 120 SER H2 H N N 121 SER HA H N N 122 SER HB2 H N N 123 SER HB3 H N N 124 SER HG H N N 125 SER HXT H N N 126 VAL N N N N 127 VAL CA C N S 128 VAL C C N N 129 VAL O O N N 130 VAL CB C N N 131 VAL CG1 C N N 132 VAL CG2 C N N 133 VAL OXT O N N 134 VAL H H N N 135 VAL H2 H N N 136 VAL HA H N N 137 VAL HB H N N 138 VAL HG11 H N N 139 VAL HG12 H N N 140 VAL HG13 H N N 141 VAL HG21 H N N 142 VAL HG22 H N N 143 VAL HG23 H N N 144 VAL HXT H N N 145 # 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 GLY N CA sing N N 29 GLY N H sing N N 30 GLY N H2 sing N N 31 GLY CA C sing N N 32 GLY CA HA2 sing N N 33 GLY CA HA3 sing N N 34 GLY C O doub N N 35 GLY C OXT sing N N 36 GLY OXT HXT sing N N 37 HOH O H1 sing N N 38 HOH O H2 sing N N 39 ILE N CA sing N N 40 ILE N H sing N N 41 ILE N H2 sing N N 42 ILE CA C sing N N 43 ILE CA CB sing N N 44 ILE CA HA sing N N 45 ILE C O doub N N 46 ILE C OXT sing N N 47 ILE CB CG1 sing N N 48 ILE CB CG2 sing N N 49 ILE CB HB sing N N 50 ILE CG1 CD1 sing N N 51 ILE CG1 HG12 sing N N 52 ILE CG1 HG13 sing N N 53 ILE CG2 HG21 sing N N 54 ILE CG2 HG22 sing N N 55 ILE CG2 HG23 sing N N 56 ILE CD1 HD11 sing N N 57 ILE CD1 HD12 sing N N 58 ILE CD1 HD13 sing N N 59 ILE OXT HXT sing N N 60 LEU N CA sing N N 61 LEU N H sing N N 62 LEU N H2 sing N N 63 LEU CA C sing N N 64 LEU CA CB sing N N 65 LEU CA HA sing N N 66 LEU C O doub N N 67 LEU C OXT sing N N 68 LEU CB CG sing N N 69 LEU CB HB2 sing N N 70 LEU CB HB3 sing N N 71 LEU CG CD1 sing N N 72 LEU CG CD2 sing N N 73 LEU CG HG sing N N 74 LEU CD1 HD11 sing N N 75 LEU CD1 HD12 sing N N 76 LEU CD1 HD13 sing N N 77 LEU CD2 HD21 sing N N 78 LEU CD2 HD22 sing N N 79 LEU CD2 HD23 sing N N 80 LEU OXT HXT sing N N 81 LYS N CA sing N N 82 LYS N H sing N N 83 LYS N H2 sing N N 84 LYS CA C sing N N 85 LYS CA CB sing N N 86 LYS CA HA sing N N 87 LYS C O doub N N 88 LYS C OXT sing N N 89 LYS CB CG sing N N 90 LYS CB HB2 sing N N 91 LYS CB HB3 sing N N 92 LYS CG CD sing N N 93 LYS CG HG2 sing N N 94 LYS CG HG3 sing N N 95 LYS CD CE sing N N 96 LYS CD HD2 sing N N 97 LYS CD HD3 sing N N 98 LYS CE NZ sing N N 99 LYS CE HE2 sing N N 100 LYS CE HE3 sing N N 101 LYS NZ HZ1 sing N N 102 LYS NZ HZ2 sing N N 103 LYS NZ HZ3 sing N N 104 LYS OXT HXT sing N N 105 SER N CA sing N N 106 SER N H sing N N 107 SER N H2 sing N N 108 SER CA C sing N N 109 SER CA CB sing N N 110 SER CA HA sing N N 111 SER C O doub N N 112 SER C OXT sing N N 113 SER CB OG sing N N 114 SER CB HB2 sing N N 115 SER CB HB3 sing N N 116 SER OG HG sing N N 117 SER OXT HXT sing N N 118 VAL N CA sing N N 119 VAL N H sing N N 120 VAL N H2 sing N N 121 VAL CA C sing N N 122 VAL CA CB sing N N 123 VAL CA HA sing N N 124 VAL C O doub N N 125 VAL C OXT sing N N 126 VAL CB CG1 sing N N 127 VAL CB CG2 sing N N 128 VAL CB HB sing N N 129 VAL CG1 HG11 sing N N 130 VAL CG1 HG12 sing N N 131 VAL CG1 HG13 sing N N 132 VAL CG2 HG21 sing N N 133 VAL CG2 HG22 sing N N 134 VAL CG2 HG23 sing N N 135 VAL OXT HXT sing N N 136 # _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.angle_alpha 90 _em_3d_crystal_entity.angle_beta 100.017 _em_3d_crystal_entity.angle_gamma 90 _em_3d_crystal_entity.length_a 18.78 _em_3d_crystal_entity.length_b 4.73 _em_3d_crystal_entity.length_c 33.47 _em_3d_crystal_entity.space_group_name 'P 21' _em_3d_crystal_entity.space_group_num 4 # loop_ _em_buffer_component.buffer_id _em_buffer_component.id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.name 1 1 25 mM ? 'citric acid' 1 2 5 % ? DMSO # _em_crystal_formation.id 1 _em_crystal_formation.specimen_id 1 _em_crystal_formation.atmosphere air _em_crystal_formation.details shaking _em_crystal_formation.instrument 'microcentrifuge tube' _em_crystal_formation.lipid_mixture ? _em_crystal_formation.lipid_protein_ratio ? _em_crystal_formation.temperature 310 _em_crystal_formation.time 2 _em_crystal_formation.time_unit DAY # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_diffraction.id 1 _em_diffraction.camera_length 1840 _em_diffraction.imaging_id 1 _em_diffraction.tilt_angle_list ? # _em_diffraction_shell.id 1 _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 47.5 _em_diffraction_shell.high_resolution 1.42 _em_diffraction_shell.low_resolution 1.49 _em_diffraction_shell.multiplicity 2.6 _em_diffraction_shell.num_structure_factors 84 _em_diffraction_shell.phase_residual 0.01 # _em_diffraction_stats.id 1 _em_diffraction_stats.details ? _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.fourier_space_coverage 85.5 _em_diffraction_stats.high_resolution 1.42 _em_diffraction_stats.num_intensities_measured 5843 _em_diffraction_stats.num_structure_factors 1129 _em_diffraction_stats.overall_phase_error 0 _em_diffraction_stats.overall_phase_residual 0.01 _em_diffraction_stats.phase_error_rejection_criteria 0 _em_diffraction_stats.r_merge 0.222 _em_diffraction_stats.r_sym 0.222 # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.ncbi_tax_id 9606 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.cell ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 0.03 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'TVIPS TEMCAM-F416 (4k x 4k)' _em_image_recording.num_diffraction_images 471 _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'IMAGE ACQUISITION' ? 'TVIPS TemCam-F416' ? ? ? 1 2 MASKING ? ? ? ? ? ? 3 'CTF CORRECTION' ? ? ? 1 ? ? 4 'LAYERLINE INDEXING' ? ? ? ? ? ? 5 'DIFFRACTION INDEXING' ? ? ? ? ? ? 6 'MODEL FITTING' ? Coot ? ? 1 ? 7 OTHER ? ? ? ? ? ? 8 'MOLECULAR REPLACEMENT' ? phaser ? 1 ? ? 9 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ? 10 'SYMMETRY DETERMINATION' ? ? ? 1 ? ? 11 'CRYSTALLOGRAPHY MERGING' ? XSCALE 'Jun 17, 2015' 1 ? ? 12 RECONSTRUCTION ? ? ? 1 ? ? 13 'MODEL REFINEMENT' ? Refmac5 ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 7.5 _em_specimen.details nanocrystals _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Howard Hughes Medical Institute (HHMI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5VOS _atom_sites.fract_transf_matrix[1][1] 0.053248 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009405 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.211416 _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] 0.030340 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O # 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 1 N N . VAL A 1 1 ? 9.585 -0.410 36.450 1.00 18.03 ? 24 VAL A N 1 ATOM 2 C CA . VAL A 1 1 ? 8.348 -1.211 36.293 1.00 17.53 ? 24 VAL A CA 1 ATOM 3 C C . VAL A 1 1 ? 7.375 -0.492 35.356 1.00 13.69 ? 24 VAL A C 1 ATOM 4 O O . VAL A 1 1 ? 7.456 0.703 35.197 1.00 13.25 ? 24 VAL A O 1 ATOM 5 C CB . VAL A 1 1 ? 7.754 -1.499 37.685 1.00 18.06 ? 24 VAL A CB 1 ATOM 6 C CG1 . VAL A 1 1 ? 7.607 -0.226 38.435 1.00 20.35 ? 24 VAL A CG1 1 ATOM 7 C CG2 . VAL A 1 1 ? 6.389 -2.147 37.632 1.00 20.65 ? 24 VAL A CG2 1 ATOM 8 N N . GLY A 1 2 ? 6.514 -1.238 34.667 1.00 10.67 ? 25 GLY A N 1 ATOM 9 C CA . GLY A 1 2 ? 5.526 -0.630 33.774 1.00 8.87 ? 25 GLY A CA 1 ATOM 10 C C . GLY A 1 2 ? 4.452 0.077 34.545 1.00 7.23 ? 25 GLY A C 1 ATOM 11 O O . GLY A 1 2 ? 4.229 1.277 34.381 1.00 7.12 ? 25 GLY A O 1 ATOM 12 N N . SER A 1 3 ? 3.788 -0.685 35.396 1.00 6.65 ? 26 SER A N 1 ATOM 13 C CA . SER A 1 3 ? 2.693 -0.181 36.209 1.00 6.64 ? 26 SER A CA 1 ATOM 14 C C . SER A 1 3 ? 2.872 -0.705 37.612 1.00 5.64 ? 26 SER A C 1 ATOM 15 O O . SER A 1 3 ? 3.074 -1.883 37.788 1.00 6.33 ? 26 SER A O 1 ATOM 16 C CB . SER A 1 3 ? 1.346 -0.647 35.627 1.00 7.02 ? 26 SER A CB 1 ATOM 17 O OG . SER A 1 3 ? 0.268 -0.552 36.548 1.00 9.40 ? 26 SER A OG 1 ATOM 18 N N . ASN A 1 4 ? 2.853 0.174 38.607 1.00 5.63 ? 27 ASN A N 1 ATOM 19 C CA . ASN A 1 4 ? 2.808 -0.290 39.974 1.00 5.53 ? 27 ASN A CA 1 ATOM 20 C C . ASN A 1 4 ? 1.560 0.286 40.581 1.00 5.96 ? 27 ASN A C 1 ATOM 21 O O . ASN A 1 4 ? 1.388 1.485 40.533 1.00 5.61 ? 27 ASN A O 1 ATOM 22 C CB . ASN A 1 4 ? 4.049 0.167 40.769 1.00 5.80 ? 27 ASN A CB 1 ATOM 23 C CG . ASN A 1 4 ? 4.150 -0.487 42.128 1.00 5.69 ? 27 ASN A CG 1 ATOM 24 O OD1 . ASN A 1 4 ? 4.076 -1.673 42.244 1.00 7.13 ? 27 ASN A OD1 1 ATOM 25 N ND2 . ASN A 1 4 ? 4.303 0.300 43.162 1.00 5.70 ? 27 ASN A ND2 1 ATOM 26 N N . LYS A 1 5 ? 0.679 -0.562 41.111 1.00 6.74 ? 28 LYS A N 1 ATOM 27 C CA . LYS A 1 5 ? -0.613 -0.107 41.660 1.00 7.37 ? 28 LYS A CA 1 ATOM 28 C C . LYS A 1 5 ? -0.782 -0.694 43.024 1.00 6.35 ? 28 LYS A C 1 ATOM 29 O O . LYS A 1 5 ? -0.649 -1.891 43.181 1.00 5.98 ? 28 LYS A O 1 ATOM 30 C CB . LYS A 1 5 ? -1.793 -0.608 40.818 1.00 10.05 ? 28 LYS A CB 1 ATOM 31 C CG . LYS A 1 5 ? -1.881 -0.124 39.397 1.00 13.08 ? 28 LYS A CG 1 ATOM 32 C CD . LYS A 1 5 ? -3.221 -0.537 38.789 1.00 15.61 ? 28 LYS A CD 1 ATOM 33 C CE . LYS A 1 5 ? -3.518 0.245 37.539 1.00 21.38 ? 28 LYS A CE 1 ATOM 34 N NZ . LYS A 1 5 ? -4.708 -0.310 36.806 1.00 21.78 ? 28 LYS A NZ 1 ATOM 35 N N . GLY A 1 6 ? -1.073 0.130 44.016 1.00 6.55 ? 29 GLY A N 1 ATOM 36 C CA . GLY A 1 6 ? -1.202 -0.406 45.339 1.00 6.36 ? 29 GLY A CA 1 ATOM 37 C C . GLY A 1 6 ? -2.292 0.271 46.105 1.00 5.27 ? 29 GLY A C 1 ATOM 38 O O . GLY A 1 6 ? -2.486 1.454 46.005 1.00 5.35 ? 29 GLY A O 1 ATOM 39 N N . ALA A 1 7 ? -2.955 -0.515 46.917 1.00 5.46 ? 30 ALA A N 1 ATOM 40 C CA . ALA A 1 7 ? -3.876 -0.026 47.906 1.00 5.33 ? 30 ALA A CA 1 ATOM 41 C C . ALA A 1 7 ? -3.483 -0.651 49.233 1.00 4.81 ? 30 ALA A C 1 ATOM 42 O O . ALA A 1 7 ? -3.435 -1.861 49.368 1.00 4.77 ? 30 ALA A O 1 ATOM 43 C CB . ALA A 1 7 ? -5.269 -0.446 47.531 1.00 6.37 ? 30 ALA A CB 1 ATOM 44 N N . ILE A 1 8 ? -3.163 0.187 50.196 1.00 5.04 ? 31 ILE A N 1 ATOM 45 C CA . ILE A 1 8 ? -2.776 -0.287 51.534 1.00 5.15 ? 31 ILE A CA 1 ATOM 46 C C . ILE A 1 8 ? -3.720 0.384 52.484 1.00 5.10 ? 31 ILE A C 1 ATOM 47 O O . ILE A 1 8 ? -3.595 1.576 52.788 1.00 4.42 ? 31 ILE A O 1 ATOM 48 C CB . ILE A 1 8 ? -1.338 0.064 51.912 1.00 5.73 ? 31 ILE A CB 1 ATOM 49 C CG1 . ILE A 1 8 ? -0.381 -0.576 50.912 1.00 6.26 ? 31 ILE A CG1 1 ATOM 50 C CG2 . ILE A 1 8 ? -1.041 -0.460 53.290 1.00 5.92 ? 31 ILE A CG2 1 ATOM 51 C CD1 . ILE A 1 8 ? 1.064 -0.295 51.191 1.00 6.96 ? 31 ILE A CD1 1 ATOM 52 N N . ILE A 1 9 ? -4.675 -0.399 52.928 1.00 5.76 ? 32 ILE A N 1 ATOM 53 C CA . ILE A 1 9 ? -5.861 0.141 53.495 1.00 6.89 ? 32 ILE A CA 1 ATOM 54 C C . ILE A 1 9 ? -6.082 -0.515 54.857 1.00 6.63 ? 32 ILE A C 1 ATOM 55 O O . ILE A 1 9 ? -6.137 -1.709 54.942 1.00 6.46 ? 32 ILE A O 1 ATOM 56 C CB . ILE A 1 9 ? -7.089 -0.100 52.574 1.00 9.87 ? 32 ILE A CB 1 ATOM 57 C CG1 . ILE A 1 9 ? -6.804 0.449 51.176 1.00 10.65 ? 32 ILE A CG1 1 ATOM 58 C CG2 . ILE A 1 9 ? -8.335 0.500 53.214 1.00 12.70 ? 32 ILE A CG2 1 ATOM 59 C CD1 . ILE A 1 9 ? -7.938 1.062 50.419 1.00 16.92 ? 32 ILE A CD1 1 ATOM 60 N N . GLY A 1 10 ? -6.206 0.306 55.895 1.00 9.17 ? 33 GLY A N 1 ATOM 61 C CA . GLY A 1 10 ? -6.577 -0.150 57.226 1.00 12.74 ? 33 GLY A CA 1 ATOM 62 C C . GLY A 1 10 ? -7.997 0.265 57.540 1.00 13.72 ? 33 GLY A C 1 ATOM 63 O O . GLY A 1 10 ? -8.306 1.453 57.515 1.00 13.74 ? 33 GLY A O 1 ATOM 64 N N . LEU A 1 11 ? -8.849 -0.728 57.792 1.00 22.20 ? 34 LEU A N 1 ATOM 65 C CA . LEU A 1 11 ? -10.201 -0.529 58.315 1.00 28.84 ? 34 LEU A CA 1 ATOM 66 C C . LEU A 1 11 ? -10.331 -1.076 59.764 1.00 27.99 ? 34 LEU A C 1 ATOM 67 O O . LEU A 1 11 ? -11.207 -0.671 60.546 1.00 28.91 ? 34 LEU A O 1 ATOM 68 C CB . LEU A 1 11 ? -11.250 -1.196 57.388 1.00 34.49 ? 34 LEU A CB 1 ATOM 69 C CG . LEU A 1 11 ? -11.866 -0.323 56.286 1.00 38.09 ? 34 LEU A CG 1 ATOM 70 C CD1 . LEU A 1 11 ? -10.749 0.182 55.404 1.00 42.18 ? 34 LEU A CD1 1 ATOM 71 C CD2 . LEU A 1 11 ? -12.895 -1.058 55.438 1.00 40.02 ? 34 LEU A CD2 1 ATOM 72 O OXT . LEU A 1 11 ? -9.592 -1.961 60.205 1.00 30.29 ? 34 LEU A OXT 1 HETATM 73 O O . HOH B 2 . ? -0.080 -2.580 37.756 1.00 15.91 ? 101 HOH A O 1 #