data_5K2E # _entry.id 5K2E # _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 5K2E pdb_00005k2e 10.2210/pdb5k2e/pdb WWPDB D_1000221567 ? ? EMDB EMD-8196 ? ? # 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 2016-09-14 2 'Structure model' 1 1 2016-09-21 3 'Structure model' 1 2 2016-10-05 4 'Structure model' 1 3 2016-10-19 5 'Structure model' 1 4 2016-11-30 6 'Structure model' 1 5 2017-09-13 7 'Structure model' 1 6 2018-04-25 8 'Structure model' 1 7 2019-11-20 9 'Structure model' 1 8 2021-06-30 10 'Structure model' 1 9 2024-03-06 # _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' 'Database references' 4 5 'Structure model' 'Refinement description' 5 6 'Structure model' 'Author supporting evidence' 6 6 'Structure model' 'Data collection' 7 7 'Structure model' 'Data collection' 8 8 'Structure model' 'Author supporting evidence' 9 9 'Structure model' 'Data collection' 10 9 'Structure model' 'Derived calculations' 11 10 'Structure model' 'Data collection' 12 10 '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 6 'Structure model' em_software 2 6 'Structure model' pdbx_audit_support 3 7 'Structure model' diffrn_source 4 8 'Structure model' pdbx_audit_support 5 9 'Structure model' diffrn_detector 6 9 'Structure model' pdbx_struct_conn_angle 7 9 'Structure model' struct_conn 8 10 'Structure model' chem_comp_atom 9 10 'Structure model' chem_comp_bond 10 10 'Structure model' database_2 # 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 6 'Structure model' '_em_software.name' 2 6 'Structure model' '_pdbx_audit_support.funding_organization' 3 7 'Structure model' '_diffrn_source.source' 4 8 'Structure model' '_pdbx_audit_support.funding_organization' 5 9 'Structure model' '_diffrn_detector.detector' 6 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 9 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 9 'Structure model' '_pdbx_struct_conn_angle.ptnr2_symmetry' 13 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 14 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 15 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 16 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 17 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 18 9 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 19 9 'Structure model' '_pdbx_struct_conn_angle.value' 20 9 'Structure model' '_struct_conn.pdbx_dist_value' 21 9 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 9 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 9 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 9 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 9 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 9 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 9 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 9 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 9 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 9 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 9 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 9 'Structure model' '_struct_conn.ptnr2_symmetry' 33 10 'Structure model' '_database_2.pdbx_DOI' 34 10 '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 5K2E _pdbx_database_status.recvd_initial_deposition_date 2016-05-18 _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 EMDB . EMD-8196 'associated EM volume' EMDB . EMD-8197 'other EM volume' EMDB . EMD-8198 'other EM volume' EMDB . EMD-8199 'other EM volume' PDB 'NNQQNY from yeast prion Sup35 with cadmium' 5K2F unspecified PDB 'GNNQQNY from yeast prion Sup35 in space group P21' 5K2G unspecified PDB 'GNNQQNY from yeast prion Sup35 in space group P212121' 5K2H unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Rodriguez, J.A.' 1 'Sawaya, M.R.' 2 'Cascio, D.' 3 'Eisenberg, D.S.' 4 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 113 _citation.language ? _citation.page_first 11232 _citation.page_last 11236 _citation.title 'Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.1606287113 _citation.pdbx_database_id_PubMed 27647903 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sawaya, M.R.' 1 ? primary 'Rodriguez, J.' 2 ? primary 'Cascio, D.' 3 ? primary 'Collazo, M.J.' 4 ? primary 'Shi, D.' 5 ? primary 'Reyes, F.E.' 6 ? primary 'Hattne, J.' 7 ? primary 'Gonen, T.' 8 ? primary 'Eisenberg, D.S.' 9 ? # 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 'Eukaryotic peptide chain release factor GTP-binding subunit' 779.755 1 ? ? 'UNP residues 8-13' ? 2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 1 ? ? ? ? 4 water nat water 18.015 6 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;SUP35, ERF-3, ERF3, ERF2, G1 to S phase transition protein 1, Omnipotent suppressor protein 2, PSI no more protein 2, Polypeptide release factor 3, Translation release factor 3 ; # _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 NNQQNY _entity_poly.pdbx_seq_one_letter_code_can NNQQNY _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 'ACETIC ACID' ACY 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASN n 1 2 ASN n 1 3 GLN n 1 4 GLN n 1 5 ASN n 1 6 TYR 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 'Saccharomyces cerevisiae' _pdbx_entity_src_syn.organism_common_name ;Baker's yeast ; _pdbx_entity_src_syn.ncbi_taxonomy_id 4932 _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 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 HOH non-polymer . WATER ? 'H2 O' 18.015 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # 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 ASN 1 1 1 ASN ASN A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 ASN 5 5 5 ASN ASN A . n A 1 6 TYR 6 6 6 TYR TYR A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ZN 1 101 7 ZN ZN A . C 3 ACY 1 102 10 ACY ACY A . D 4 HOH 1 201 3 HOH HOH A . D 4 HOH 2 202 2 HOH HOH A . D 4 HOH 3 203 5 HOH HOH A . D 4 HOH 4 204 4 HOH HOH A . D 4 HOH 5 205 6 HOH HOH A . D 4 HOH 6 206 1 HOH HOH A . # 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 collection' ? ? 'Zbyszek Otwinowski' hkl@hkl-xray.com ? ? ? ? ? http://www.hkl-xray.com/ ? DENZO ? ? program . 1 ? 'data scaling' ? ? 'Zbyszek Otwinowski' hkl@hkl-xray.com ? ? ? ? ? http://www.hkl-xray.com/ ? SCALEPACK ? ? 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 'June. 20, 2015' ? ? ? C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.20 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 103.950 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5K2E _cell.details ? _cell.formula_units_Z ? _cell.length_a 21.480 _cell.length_a_esd ? _cell.length_b 4.950 _cell.length_b_esd ? _cell.length_c 23.870 _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 5K2E _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 5K2E _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews ? _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 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 273 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M zinc sulfate' _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 2016-02-03 # _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 ? _reflns.entry_id 5K2E _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.000 _reflns.d_resolution_low 90.000 _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 2712 _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 85.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 4.900 _reflns.pdbx_Rmerge_I_obs 0.211 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 5.767 _reflns.pdbx_netI_over_sigmaI 4.100 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.051 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 13199 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # 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 1.000 1.080 ? ? ? ? ? 460 ? 79.900 ? ? ? ? 0.362 ? ? ? ? ? ? ? ? 3.000 ? 1.016 ? ? ? ? 0 1 1 ? ? 1.080 1.190 ? ? ? ? ? 541 ? 85.900 ? ? ? ? 0.293 ? ? ? ? ? ? ? ? 4.800 ? 1.007 ? ? ? ? 0 2 1 ? ? 1.190 1.360 ? ? ? ? ? 533 ? 87.500 ? ? ? ? 0.278 ? ? ? ? ? ? ? ? 5.000 ? 0.976 ? ? ? ? 0 3 1 ? ? 1.360 1.710 ? ? ? ? ? 581 ? 89.500 ? ? ? ? 0.231 ? ? ? ? ? ? ? ? 5.900 ? 1.027 ? ? ? ? 0 4 1 ? ? 1.710 90.000 ? ? ? ? ? 597 ? 85.800 ? ? ? ? 0.154 ? ? ? ? ? ? ? ? 5.300 ? 1.187 ? ? ? ? 0 5 1 ? ? # _refine.aniso_B[1][1] -0.0400 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 0.0100 _refine.aniso_B[2][2] -0.3000 _refine.aniso_B[2][3] -0.0000 _refine.aniso_B[3][3] 0.2900 _refine.B_iso_max 23.950 _refine.B_iso_mean 4.4450 _refine.B_iso_min 2.990 _refine.correlation_coeff_Fo_to_Fc 0.9550 _refine.correlation_coeff_Fo_to_Fc_free 0.9120 _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _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 5K2E _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 1.0000 _refine.ls_d_res_low 23.1700 _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 2124 _refine.ls_number_reflns_R_free 234 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 79.5000 _refine.ls_percent_reflns_R_free 9.9000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1564 _refine.ls_R_factor_R_free 0.1943 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1523 _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 ? _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 0.0350 _refine.pdbx_overall_ESU_R_Free 0.0380 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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 1.7460 _refine.overall_SU_ML 0.0390 _refine.overall_SU_R_Cruickshank_DPI 0.0353 _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 1.0000 _refine_hist.d_res_low 23.1700 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 69 _refine_hist.pdbx_number_residues_total 6 _refine_hist.pdbx_B_iso_mean_ligand 4.02 _refine_hist.pdbx_B_iso_mean_solvent 12.88 _refine_hist.pdbx_number_atoms_protein 55 _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' ? 0.020 0.020 58 ? r_bond_refined_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.006 0.020 45 ? r_bond_other_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.525 1.892 77 ? r_angle_refined_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.895 3.000 98 ? r_angle_other_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 7.311 5.000 5 ? r_dihedral_angle_1_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 61.713 28.333 6 ? r_dihedral_angle_2_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 9.350 15.000 8 ? r_dihedral_angle_3_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.101 0.200 6 ? r_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.005 0.020 81 ? r_gen_planes_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.000 0.020 19 ? r_gen_planes_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.267 0.345 24 ? r_mcbond_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.222 0.339 22 ? r_mcbond_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.312 0.515 27 ? r_mcangle_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.337 3.000 103 ? r_rigid_bond_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 28.654 5.000 1 ? r_sphericity_free ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 2.873 5.000 110 ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine_ls_shell.d_res_high 0.9970 _refine_ls_shell.d_res_low 1.0230 _refine_ls_shell.number_reflns_all 60 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 8 _refine_ls_shell.number_reflns_R_work 52 _refine_ls_shell.percent_reflns_obs 31.4100 _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 0.1470 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.1670 _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 5K2E _struct.title 'Structure of NNQQNY from yeast prion Sup35 with zinc acetate 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 5K2E _struct_keywords.text 'amyloid, yeast prion, 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 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ERF3_YEAST _struct_ref.pdbx_db_accession P05453 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code NNQQNY _struct_ref.pdbx_align_begin 8 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5K2E _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 P05453 _struct_ref_seq.db_align_beg 8 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 13 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 # 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,D 1 2 A,B,C,D 1 3 A,B,C,D 1 4 A,B,C,D 1 5 A,B,C,D 1 6 A,B,C,D 1 7 A,B,C,D 1 8 A,B,C,D 1 9 A,B,C,D 1 10 A,B,C,D 1 11 A,B,C,D 1 12 A,B,C,D 1 13 A,B,C,D 1 14 A,B,C,D 1 15 A,B,C,D 1 16 A,B,C,D 1 17 A,B,C,D 1 18 A,B,C,D # 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_515 x,y-4,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -19.8000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_525 x,y-3,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -14.8500000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_535 x,y-2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -9.9000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 1_545 x,y-1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -4.9500000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.9500000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 7 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9.9000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 8 'crystal symmetry operation' 1_585 x,y+3,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 14.8500000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9 'crystal symmetry operation' 1_595 x,y+4,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 19.8000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 10 'crystal symmetry operation' 2_515 -x,y-7/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -17.3250000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 11 'crystal symmetry operation' 2_525 -x,y-5/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -12.3750000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 12 'crystal symmetry operation' 2_535 -x,y-3/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -7.4250000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 13 'crystal symmetry operation' 2_545 -x,y-1/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -2.4750000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 14 'crystal symmetry operation' 2_555 -x,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2.4750000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 15 'crystal symmetry operation' 2_565 -x,y+3/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 7.4250000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 16 'crystal symmetry operation' 2_575 -x,y+5/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 12.3750000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 17 'crystal symmetry operation' 2_585 -x,y+7/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 17.3250000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 18 'crystal symmetry operation' 2_595 -x,y+9/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 22.2750000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ;The biological unit is an extended pair of beta sheets comprising peptides at positions X,Y,Z and -X,Y+1/2,-Z extended ad infinitum along the b crystal axis. ; # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A ASN 1 N ? ? ? 1_555 B ZN . ZN ? ? A ASN 1 A ZN 101 1_455 ? ? ? ? ? ? ? 2.157 ? ? metalc2 metalc ? ? A TYR 6 O ? ? ? 1_555 B ZN . ZN ? ? A TYR 6 A ZN 101 1_555 ? ? ? ? ? ? ? 2.036 ? ? metalc3 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACY . OXT ? ? A ZN 101 A ACY 102 1_555 ? ? ? ? ? ? ? 2.032 ? ? metalc4 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACY . O ? ? A ZN 101 A ACY 102 1_565 ? ? ? ? ? ? ? 1.987 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N ? A ASN 1 ? A ASN 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 O ? A TYR 6 ? A TYR 6 ? 1_555 81.1 ? 2 N ? A ASN 1 ? A ASN 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 OXT ? C ACY . ? A ACY 102 ? 1_555 82.8 ? 3 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 OXT ? C ACY . ? A ACY 102 ? 1_555 2.3 ? 4 N ? A ASN 1 ? A ASN 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 O ? C ACY . ? A ACY 102 ? 1_565 81.9 ? 5 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 O ? C ACY . ? A ACY 102 ? 1_565 6.6 ? 6 OXT ? C ACY . ? A ACY 102 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_455 O ? C ACY . ? A ACY 102 ? 1_565 8.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ZN 101 ? 2 'binding site for residue ZN A 101' AC2 Software A ACY 102 ? 2 'binding site for residue ACY A 102' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 TYR A 6 ? TYR A 6 . ? 1_555 ? 2 AC1 2 ACY C . ? ACY A 102 . ? 1_555 ? 3 AC2 2 TYR A 6 ? TYR A 6 . ? 1_555 ? 4 AC2 2 ZN B . ? ZN A 101 . ? 1_555 ? # _em_3d_fitting.entry_id 5K2E _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value 4.4 _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 5K2E _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ;The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD. ; _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 7 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'Prion fibril composed of a 6-residue segment of Sup35 and zinc' _em_entity_assembly.source 'MULTIPLE SOURCES' _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 5K2E _em_image_scans.id 1 _em_image_scans.dimension_height 4096 _em_image_scans.dimension_width 4096 _em_image_scans.frames_per_image ? _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size 15.6 _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image ? _em_image_scans.number_digital_images ? _em_image_scans.details ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.citation_id ? # _em_imaging.id 1 _em_imaging.entry_id 5K2E _em_imaging.accelerating_voltage 200 _em_imaging.alignment_procedure BASIC _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 100 _em_imaging.recording_temperature_minimum 100 _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.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.specimen_holder_type ? _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.citation_id ? _em_imaging.detector_distance ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R2/2' _em_sample_support.method ? _em_sample_support.film_material ? _em_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 'Plunged into liquid ethane (FEI VITROBOT MARK IV)' _em_vitrification.humidity ? _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 5K2E _em_vitrification.temp ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? # _em_experiment.entry_id 5K2E _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 ACY C C N N 1 ACY O O N N 2 ACY OXT O N N 3 ACY CH3 C N N 4 ACY HXT H N N 5 ACY H1 H N N 6 ACY H2 H N N 7 ACY H3 H N N 8 ASN N N N N 9 ASN CA C N S 10 ASN C C N N 11 ASN O O N N 12 ASN CB C N N 13 ASN CG C N N 14 ASN OD1 O N N 15 ASN ND2 N N N 16 ASN OXT O N N 17 ASN H H N N 18 ASN H2 H N N 19 ASN HA H N N 20 ASN HB2 H N N 21 ASN HB3 H N N 22 ASN HD21 H N N 23 ASN HD22 H N N 24 ASN HXT H N N 25 GLN N N N N 26 GLN CA C N S 27 GLN C C N N 28 GLN O O N N 29 GLN CB C N N 30 GLN CG C N N 31 GLN CD C N N 32 GLN OE1 O N N 33 GLN NE2 N N N 34 GLN OXT O N N 35 GLN H H N N 36 GLN H2 H N N 37 GLN HA H N N 38 GLN HB2 H N N 39 GLN HB3 H N N 40 GLN HG2 H N N 41 GLN HG3 H N N 42 GLN HE21 H N N 43 GLN HE22 H N N 44 GLN HXT H N N 45 HOH O O N N 46 HOH H1 H N N 47 HOH H2 H N N 48 TYR N N N N 49 TYR CA C N S 50 TYR C C N N 51 TYR O O N N 52 TYR CB C N N 53 TYR CG C Y N 54 TYR CD1 C Y N 55 TYR CD2 C Y N 56 TYR CE1 C Y N 57 TYR CE2 C Y N 58 TYR CZ C Y N 59 TYR OH O N N 60 TYR OXT O N N 61 TYR H H N N 62 TYR H2 H N N 63 TYR HA H N N 64 TYR HB2 H N N 65 TYR HB3 H N N 66 TYR HD1 H N N 67 TYR HD2 H N N 68 TYR HE1 H N N 69 TYR HE2 H N N 70 TYR HH H N N 71 TYR HXT H N N 72 ZN ZN ZN N N 73 # 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 ACY C O doub N N 1 ACY C OXT sing N N 2 ACY C CH3 sing N N 3 ACY OXT HXT sing N N 4 ACY CH3 H1 sing N N 5 ACY CH3 H2 sing N N 6 ACY CH3 H3 sing N N 7 ASN N CA sing N N 8 ASN N H sing N N 9 ASN N H2 sing N N 10 ASN CA C sing N N 11 ASN CA CB sing N N 12 ASN CA HA sing N N 13 ASN C O doub N N 14 ASN C OXT sing N N 15 ASN CB CG sing N N 16 ASN CB HB2 sing N N 17 ASN CB HB3 sing N N 18 ASN CG OD1 doub N N 19 ASN CG ND2 sing N N 20 ASN ND2 HD21 sing N N 21 ASN ND2 HD22 sing N N 22 ASN OXT HXT sing N N 23 GLN N CA sing N N 24 GLN N H sing N N 25 GLN N H2 sing N N 26 GLN CA C sing N N 27 GLN CA CB sing N N 28 GLN CA HA sing N N 29 GLN C O doub N N 30 GLN C OXT sing N N 31 GLN CB CG sing N N 32 GLN CB HB2 sing N N 33 GLN CB HB3 sing N N 34 GLN CG CD sing N N 35 GLN CG HG2 sing N N 36 GLN CG HG3 sing N N 37 GLN CD OE1 doub N N 38 GLN CD NE2 sing N N 39 GLN NE2 HE21 sing N N 40 GLN NE2 HE22 sing N N 41 GLN OXT HXT sing N N 42 HOH O H1 sing N N 43 HOH O H2 sing N N 44 TYR N CA sing N N 45 TYR N H sing N N 46 TYR N H2 sing N N 47 TYR CA C sing N N 48 TYR CA CB sing N N 49 TYR CA HA sing N N 50 TYR C O doub N N 51 TYR C OXT sing N N 52 TYR CB CG sing N N 53 TYR CB HB2 sing N N 54 TYR CB HB3 sing N N 55 TYR CG CD1 doub Y N 56 TYR CG CD2 sing Y N 57 TYR CD1 CE1 sing Y N 58 TYR CD1 HD1 sing N N 59 TYR CD2 CE2 doub Y N 60 TYR CD2 HD2 sing N N 61 TYR CE1 CZ doub Y N 62 TYR CE1 HE1 sing N N 63 TYR CE2 CZ sing Y N 64 TYR CE2 HE2 sing N N 65 TYR CZ OH sing N N 66 TYR OH HH sing N N 67 TYR OXT HXT sing N N 68 # _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 104.0 _em_3d_crystal_entity.angle_gamma 90 _em_3d_crystal_entity.length_a 21.5 _em_3d_crystal_entity.length_b 4.9 _em_3d_crystal_entity.length_c 23.9 _em_3d_crystal_entity.space_group_name 'P 1 21 1' _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 0.1 M C8H18N2O4S HEPES 1 2 1.0 M NaC2H3O2 'sodium acetate' 1 3 0.01 M ZnSO4 'zinc sulfate' # _em_crystal_formation.id 1 _em_crystal_formation.specimen_id 1 _em_crystal_formation.atmosphere 'in air, in sealed chamber, in equilibrium with reservoir solution' _em_crystal_formation.details ;Crystals were grown by hanging-drop vapor diffusion at ~20 degrees C. The reservoir solution contained 100 mM HEPES, pH 7.0, and 1 M sodium acetate (pH not adjusted). Drops were prepared by pipetting 5 microliters of 30 mg/mL aqueous peptide solution, 4 microliters of reservoir solution, and 1 microliter of 0.1 M zinc sulfate onto a glass coverslip. Crystals grew within a day. ; _em_crystal_formation.instrument '24-well plate' _em_crystal_formation.lipid_mixture none _em_crystal_formation.lipid_protein_ratio ? _em_crystal_formation.temperature 298 _em_crystal_formation.time 1 _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 1350 _em_diffraction.imaging_id 1 _em_diffraction.tilt_angle_list ? # loop_ _em_diffraction_shell.id _em_diffraction_shell.em_diffraction_stats_id _em_diffraction_shell.fourier_space_coverage _em_diffraction_shell.high_resolution _em_diffraction_shell.low_resolution _em_diffraction_shell.multiplicity _em_diffraction_shell.num_structure_factors _em_diffraction_shell.phase_residual 1 1 85.8 1.71 90 5.3 597 0.1 2 1 89.5 1.36 1.71 5.9 581 0.1 3 1 87.5 1.19 1.36 5.0 533 0.1 4 1 85.9 1.08 1.19 4.8 541 0.1 5 1 79.9 1.00 1.08 3.0 460 0.1 # _em_diffraction_stats.id 1 _em_diffraction_stats.details ;Phase statistics are not applicable. No imaging was used. The phases were obtained by a crystallographic direct methods program, SHELXD. ; _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.fourier_space_coverage 82.7 _em_diffraction_stats.high_resolution 1.00 _em_diffraction_stats.num_intensities_measured 16753 _em_diffraction_stats.num_structure_factors 2399 _em_diffraction_stats.overall_phase_error 0.1 _em_diffraction_stats.overall_phase_residual 0.1 _em_diffraction_stats.phase_error_rejection_criteria 0 _em_diffraction_stats.r_merge 15.1 _em_diffraction_stats.r_sym 15.1 # _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 KILODALTONS/NANOMETER _em_entity_assembly_molwt.value 3.25 # _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 4932 _em_entity_assembly_naturalsource.organ . _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Saccharomyces cerevisiae' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue . # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 0.01 _em_image_recording.average_exposure_time 2 _em_image_recording.details 'The detector was operated in rolling shutter mode with 2x2 pixel binning.' _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'TVIPS TEMCAM-F416 (4k x 4k)' _em_image_recording.num_diffraction_images 879 _em_image_recording.num_grids_imaged 2 _em_image_recording.num_real_images ? # _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_name none _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'IMAGE ACQUISITION' ? EM-Menu ? ? ? 1 2 MASKING ? ? ? ? ? ? 3 'CTF CORRECTION' ? ? ? 1 ? ? 4 'LAYERLINE INDEXING' ? ? ? ? ? ? 5 'DIFFRACTION INDEXING' ? Denzo 1.98.7 ? ? ? 6 'MODEL FITTING' ? Coot 0.8.2 ? 1 ? 7 OTHER phasing SHELXD 2013/2 ? ? ? 8 'MODEL REFINEMENT' ? refmac5 5.8.0135 ? 1 ? 9 'MOLECULAR REPLACEMENT' ? ? ? 1 ? ? 10 'SYMMETRY DETERMINATION' ? ? ? 1 ? ? 11 'CRYSTALLOGRAPHY MERGING' ? SCALEPACK 1.98.7 1 ? ? 12 RECONSTRUCTION 'direct methods' SHELXD 2013/2 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 30 _em_specimen.details crystal _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, United States)' 'United States' MCB-0445429 1 'National Institutes of Health/National Institute on Aging (NIH/NIA)' 'United States' 1R01-AG029430 2 ;Alzheimer's Disease Reasearch Center ; 'United States' ? 3 'Howard Hughes Medical Institute (HHMI)' 'United States' ? 4 'Department of Energy (DOE, United States)' 'United States' DE-FC02-02ER63421 5 'Giannini Foundation' 'United States' ? 6 # _atom_sites.entry_id 5K2E _atom_sites.fract_transf_matrix[1][1] 0.046555 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.011566 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.202020 _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] 0.043167 _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 H N O ZN # loop_