data_8JVQ # _entry.id 8JVQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8JVQ pdb_00008jvq 10.2210/pdb8jvq/pdb WWPDB D_1300038838 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2024-07-03 2 'Structure model' 1 1 2024-08-07 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.page_first' 7 2 'Structure model' '_citation.page_last' 8 2 'Structure model' '_citation.pdbx_database_id_DOI' 9 2 'Structure model' '_citation.pdbx_database_id_PubMed' 10 2 'Structure model' '_citation.title' 11 2 'Structure model' '_citation.year' 12 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8JVQ _pdbx_database_status.recvd_initial_deposition_date 2023-06-28 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email shunsuke.tagami@riken.jp _pdbx_contact_author.name_first Shunsuke _pdbx_contact_author.name_last Tagami _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-1720-3627 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Yagi, S.' 1 ? 'Tagami, S.' 2 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 15 _citation.language ? _citation.page_first 5938 _citation.page_last 5938 _citation.title 'An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-024-50013-9 _citation.pdbx_database_id_PubMed 39025855 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yagi, S.' 1 0000-0002-7117-3318 primary 'Tagami, S.' 2 0000-0002-1720-3627 # 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 man Ph1_DG 4681.695 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 non-polymer syn 'CITRIC ACID' 192.124 1 ? ? ? ? 4 water nat water 18.015 40 ? ? ? ? # _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 GPMPGKKFVARVAEADGKRVVIIPKAERAKVGIKVGDVVEVKKV _entity_poly.pdbx_seq_one_letter_code_can GPMPGKKFVARVAEADGKRVVIIPKAERAKVGIKVGDVVEVKKV _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 'SULFATE ION' SO4 3 'CITRIC ACID' CIT 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 PRO n 1 3 MET n 1 4 PRO n 1 5 GLY n 1 6 LYS n 1 7 LYS n 1 8 PHE n 1 9 VAL n 1 10 ALA n 1 11 ARG n 1 12 VAL n 1 13 ALA n 1 14 GLU n 1 15 ALA n 1 16 ASP n 1 17 GLY n 1 18 LYS n 1 19 ARG n 1 20 VAL n 1 21 VAL n 1 22 ILE n 1 23 ILE n 1 24 PRO n 1 25 LYS n 1 26 ALA n 1 27 GLU n 1 28 ARG n 1 29 ALA n 1 30 LYS n 1 31 VAL n 1 32 GLY n 1 33 ILE n 1 34 LYS n 1 35 VAL n 1 36 GLY n 1 37 ASP n 1 38 VAL n 1 39 VAL n 1 40 GLU n 1 41 VAL n 1 42 LYS n 1 43 LYS n 1 44 VAL n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 44 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CIT non-polymer . 'CITRIC ACID' ? 'C6 H8 O7' 192.124 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 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 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 GLY 1 1 1 GLY GLY A . n A 1 2 PRO 2 2 2 PRO PRO A . n A 1 3 MET 3 3 3 MET MET A . n A 1 4 PRO 4 4 4 PRO PRO A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 PHE 8 8 8 PHE PHE A . n A 1 9 VAL 9 9 9 VAL VAL A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 VAL 12 12 12 VAL VAL A . n A 1 13 ALA 13 13 13 ALA ALA A . n A 1 14 GLU 14 14 14 GLU GLU A . n A 1 15 ALA 15 15 15 ALA ALA A . n A 1 16 ASP 16 16 16 ASP ASP A . n A 1 17 GLY 17 17 17 GLY GLY A . n A 1 18 LYS 18 18 18 LYS LYS A . n A 1 19 ARG 19 19 19 ARG ARG A . n A 1 20 VAL 20 20 20 VAL VAL A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 ILE 22 22 22 ILE ILE A . n A 1 23 ILE 23 23 23 ILE ILE A . n A 1 24 PRO 24 24 24 PRO PRO A . n A 1 25 LYS 25 25 25 LYS LYS A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 ARG 28 28 28 ARG ARG A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 LYS 30 30 30 LYS LYS A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 GLY 32 32 32 GLY GLY A . n A 1 33 ILE 33 33 33 ILE ILE A . n A 1 34 LYS 34 34 34 LYS LYS A . n A 1 35 VAL 35 35 35 VAL VAL A . n A 1 36 GLY 36 36 36 GLY GLY A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 VAL 38 38 38 VAL VAL A . n A 1 39 VAL 39 39 39 VAL VAL A . n A 1 40 GLU 40 40 40 GLU GLU A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 LYS 42 42 42 LYS LYS A . n A 1 43 LYS 43 43 43 LYS LYS A . n A 1 44 VAL 44 44 44 VAL VAL 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 SO4 1 101 1 SO4 SO4 A . C 3 CIT 1 102 101 CIT CIT A . D 4 HOH 1 201 25 HOH HOH A . D 4 HOH 2 202 33 HOH HOH A . D 4 HOH 3 203 8 HOH HOH A . D 4 HOH 4 204 34 HOH HOH A . D 4 HOH 5 205 10 HOH HOH A . D 4 HOH 6 206 3 HOH HOH A . D 4 HOH 7 207 39 HOH HOH A . D 4 HOH 8 208 35 HOH HOH A . D 4 HOH 9 209 12 HOH HOH A . D 4 HOH 10 210 36 HOH HOH A . D 4 HOH 11 211 31 HOH HOH A . D 4 HOH 12 212 6 HOH HOH A . D 4 HOH 13 213 14 HOH HOH A . D 4 HOH 14 214 2 HOH HOH A . D 4 HOH 15 215 15 HOH HOH A . D 4 HOH 16 216 26 HOH HOH A . D 4 HOH 17 217 4 HOH HOH A . D 4 HOH 18 218 22 HOH HOH A . D 4 HOH 19 219 1 HOH HOH A . D 4 HOH 20 220 17 HOH HOH A . D 4 HOH 21 221 5 HOH HOH A . D 4 HOH 22 222 19 HOH HOH A . D 4 HOH 23 223 7 HOH HOH A . D 4 HOH 24 224 23 HOH HOH A . D 4 HOH 25 225 11 HOH HOH A . D 4 HOH 26 226 38 HOH HOH A . D 4 HOH 27 227 40 HOH HOH A . D 4 HOH 28 228 32 HOH HOH A . D 4 HOH 29 229 28 HOH HOH A . D 4 HOH 30 230 37 HOH HOH A . D 4 HOH 31 231 27 HOH HOH A . D 4 HOH 32 232 13 HOH HOH A . D 4 HOH 33 233 30 HOH HOH A . D 4 HOH 34 234 18 HOH HOH A . D 4 HOH 35 235 21 HOH HOH A . D 4 HOH 36 236 20 HOH HOH A . D 4 HOH 37 237 29 HOH HOH A . D 4 HOH 38 238 16 HOH HOH A . D 4 HOH 39 239 9 HOH HOH A . D 4 HOH 40 240 42 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 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.14_3260: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 8JVQ _cell.details ? _cell.formula_units_Z ? _cell.length_a 35.017 _cell.length_a_esd ? _cell.length_b 35.017 _cell.length_b_esd ? _cell.length_c 54.660 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8JVQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 8JVQ _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.07 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 40.47 _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.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '3200mM Ammonium sulfate, 100mM Citric acid/Sodium hydroxide pH5.0' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RAYONIX MX-225' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-04-22 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SPRING-8 BEAMLINE BL26B2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL26B2 _diffrn_source.pdbx_synchrotron_site SPring-8 # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8JVQ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.4 _reflns.d_resolution_low 50 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 14659 _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 99.2 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 11.1 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.45 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.0 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 1.4 _reflns_shell.d_res_low 1.5 _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 2362 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.99 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8JVQ _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.401 _refine.ls_d_res_low 26.518 _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 14649 _refine.ls_number_reflns_R_free 674 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.39 _refine.ls_percent_reflns_R_free 4.60 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2135 _refine.ls_R_factor_R_free 0.2409 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2122 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 28.13 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.14 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.401 _refine_hist.d_res_low 26.518 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 386 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 328 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.017 ? 355 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.280 ? 478 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 26.488 ? 142 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.092 ? 54 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.006 ? 61 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.4012 1.5094 . . 119 2849 100.00 . . . . 0.2635 . . . . . . . . . . . 0.2658 'X-RAY DIFFRACTION' 1.5094 1.6613 . . 127 2809 100.00 . . . . 0.2659 . . . . . . . . . . . 0.2473 'X-RAY DIFFRACTION' 1.6613 1.9016 . . 156 2760 100.00 . . . . 0.2689 . . . . . . . . . . . 0.3093 'X-RAY DIFFRACTION' 1.9016 2.3956 . . 138 2819 100.00 . . . . 0.2160 . . . . . . . . . . . 0.2161 'X-RAY DIFFRACTION' 2.3956 26.518 . . 134 2738 97.00 . . . . 0.1867 . . . . . . . . . . . 0.2308 # _struct.entry_id 8JVQ _struct.title 'Crystal structure of the dimeric RIFT fold protein Ph1_DG' _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 8JVQ _struct_keywords.text 'RIFT barrel, DNA BINDING PROTEIN' _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' # 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 PDB _struct_ref.db_code 8JVQ _struct_ref.pdbx_db_accession 8JVQ _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8JVQ _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 44 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8JVQ _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 44 _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 44 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3980 ? 1 MORE -43 ? 1 'SSA (A^2)' 6030 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _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' 5_555 x-y,-y,-z+1/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 18.2200000000 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id PRO _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 24 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLY _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 32 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id PRO _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 24 _struct_conf.end_auth_comp_id GLY _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 32 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id AA1 _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 ALA A 13 ? ALA A 15 ? ALA A 13 ALA A 15 AA1 2 LYS A 18 ? VAL A 20 ? LYS A 18 VAL A 20 # _pdbx_struct_sheet_hbond.sheet_id AA1 _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id ALA _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 13 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id ALA _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 13 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id VAL _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 20 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id VAL _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 20 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CD _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 GLU _pdbx_validate_rmsd_bond.auth_seq_id_1 40 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 OE2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 GLU _pdbx_validate_rmsd_bond.auth_seq_id_2 40 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.181 _pdbx_validate_rmsd_bond.bond_target_value 1.252 _pdbx_validate_rmsd_bond.bond_deviation -0.071 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.011 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 233 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_entry_details.entry_id 8JVQ _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification ? # 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 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASP N N N N 41 ASP CA C N S 42 ASP C C N N 43 ASP O O N N 44 ASP CB C N N 45 ASP CG C N N 46 ASP OD1 O N N 47 ASP OD2 O N N 48 ASP OXT O N N 49 ASP H H N N 50 ASP H2 H N N 51 ASP HA H N N 52 ASP HB2 H N N 53 ASP HB3 H N N 54 ASP HD2 H N N 55 ASP HXT H N N 56 CIT C1 C N N 57 CIT O1 O N N 58 CIT O2 O N N 59 CIT C2 C N N 60 CIT C3 C N N 61 CIT O7 O N N 62 CIT C4 C N N 63 CIT C5 C N N 64 CIT O3 O N N 65 CIT O4 O N N 66 CIT C6 C N N 67 CIT O5 O N N 68 CIT O6 O N N 69 CIT HO2 H N N 70 CIT H21 H N N 71 CIT H22 H N N 72 CIT HO7 H N N 73 CIT H41 H N N 74 CIT H42 H N N 75 CIT HO4 H N N 76 CIT HO6 H N N 77 GLU N N N N 78 GLU CA C N S 79 GLU C C N N 80 GLU O O N N 81 GLU CB C N N 82 GLU CG C N N 83 GLU CD C N N 84 GLU OE1 O N N 85 GLU OE2 O N N 86 GLU OXT O N N 87 GLU H H N N 88 GLU H2 H N N 89 GLU HA H N N 90 GLU HB2 H N N 91 GLU HB3 H N N 92 GLU HG2 H N N 93 GLU HG3 H N N 94 GLU HE2 H N N 95 GLU HXT H N N 96 GLY N N N N 97 GLY CA C N N 98 GLY C C N N 99 GLY O O N N 100 GLY OXT O N N 101 GLY H H N N 102 GLY H2 H N N 103 GLY HA2 H N N 104 GLY HA3 H N N 105 GLY HXT H N N 106 HOH O O N N 107 HOH H1 H N N 108 HOH H2 H N N 109 ILE N N N N 110 ILE CA C N S 111 ILE C C N N 112 ILE O O N N 113 ILE CB C N S 114 ILE CG1 C N N 115 ILE CG2 C N N 116 ILE CD1 C N N 117 ILE OXT O N N 118 ILE H H N N 119 ILE H2 H N N 120 ILE HA H N N 121 ILE HB H N N 122 ILE HG12 H N N 123 ILE HG13 H N N 124 ILE HG21 H N N 125 ILE HG22 H N N 126 ILE HG23 H N N 127 ILE HD11 H N N 128 ILE HD12 H N N 129 ILE HD13 H N N 130 ILE HXT H N N 131 LYS N N N N 132 LYS CA C N S 133 LYS C C N N 134 LYS O O N N 135 LYS CB C N N 136 LYS CG C N N 137 LYS CD C N N 138 LYS CE C N N 139 LYS NZ N N N 140 LYS OXT O N N 141 LYS H H N N 142 LYS H2 H N N 143 LYS HA H N N 144 LYS HB2 H N N 145 LYS HB3 H N N 146 LYS HG2 H N N 147 LYS HG3 H N N 148 LYS HD2 H N N 149 LYS HD3 H N N 150 LYS HE2 H N N 151 LYS HE3 H N N 152 LYS HZ1 H N N 153 LYS HZ2 H N N 154 LYS HZ3 H N N 155 LYS HXT H N N 156 MET N N N N 157 MET CA C N S 158 MET C C N N 159 MET O O N N 160 MET CB C N N 161 MET CG C N N 162 MET SD S N N 163 MET CE C N N 164 MET OXT O N N 165 MET H H N N 166 MET H2 H N N 167 MET HA H N N 168 MET HB2 H N N 169 MET HB3 H N N 170 MET HG2 H N N 171 MET HG3 H N N 172 MET HE1 H N N 173 MET HE2 H N N 174 MET HE3 H N N 175 MET HXT H N N 176 PHE N N N N 177 PHE CA C N S 178 PHE C C N N 179 PHE O O N N 180 PHE CB C N N 181 PHE CG C Y N 182 PHE CD1 C Y N 183 PHE CD2 C Y N 184 PHE CE1 C Y N 185 PHE CE2 C Y N 186 PHE CZ C Y N 187 PHE OXT O N N 188 PHE H H N N 189 PHE H2 H N N 190 PHE HA H N N 191 PHE HB2 H N N 192 PHE HB3 H N N 193 PHE HD1 H N N 194 PHE HD2 H N N 195 PHE HE1 H N N 196 PHE HE2 H N N 197 PHE HZ H N N 198 PHE HXT H N N 199 PRO N N N N 200 PRO CA C N S 201 PRO C C N N 202 PRO O O N N 203 PRO CB C N N 204 PRO CG C N N 205 PRO CD C N N 206 PRO OXT O N N 207 PRO H H N N 208 PRO HA H N N 209 PRO HB2 H N N 210 PRO HB3 H N N 211 PRO HG2 H N N 212 PRO HG3 H N N 213 PRO HD2 H N N 214 PRO HD3 H N N 215 PRO HXT H N N 216 SO4 S S N N 217 SO4 O1 O N N 218 SO4 O2 O N N 219 SO4 O3 O N N 220 SO4 O4 O N N 221 VAL N N N N 222 VAL CA C N S 223 VAL C C N N 224 VAL O O N N 225 VAL CB C N N 226 VAL CG1 C N N 227 VAL CG2 C N N 228 VAL OXT O N N 229 VAL H H N N 230 VAL H2 H N N 231 VAL HA H N N 232 VAL HB H N N 233 VAL HG11 H N N 234 VAL HG12 H N N 235 VAL HG13 H N N 236 VAL HG21 H N N 237 VAL HG22 H N N 238 VAL HG23 H N N 239 VAL HXT H N N 240 # 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 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASP N CA sing N N 39 ASP N H sing N N 40 ASP N H2 sing N N 41 ASP CA C sing N N 42 ASP CA CB sing N N 43 ASP CA HA sing N N 44 ASP C O doub N N 45 ASP C OXT sing N N 46 ASP CB CG sing N N 47 ASP CB HB2 sing N N 48 ASP CB HB3 sing N N 49 ASP CG OD1 doub N N 50 ASP CG OD2 sing N N 51 ASP OD2 HD2 sing N N 52 ASP OXT HXT sing N N 53 CIT C1 O1 doub N N 54 CIT C1 O2 sing N N 55 CIT C1 C2 sing N N 56 CIT O2 HO2 sing N N 57 CIT C2 C3 sing N N 58 CIT C2 H21 sing N N 59 CIT C2 H22 sing N N 60 CIT C3 O7 sing N N 61 CIT C3 C4 sing N N 62 CIT C3 C6 sing N N 63 CIT O7 HO7 sing N N 64 CIT C4 C5 sing N N 65 CIT C4 H41 sing N N 66 CIT C4 H42 sing N N 67 CIT C5 O3 doub N N 68 CIT C5 O4 sing N N 69 CIT O4 HO4 sing N N 70 CIT C6 O5 doub N N 71 CIT C6 O6 sing N N 72 CIT O6 HO6 sing N N 73 GLU N CA sing N N 74 GLU N H sing N N 75 GLU N H2 sing N N 76 GLU CA C sing N N 77 GLU CA CB sing N N 78 GLU CA HA sing N N 79 GLU C O doub N N 80 GLU C OXT sing N N 81 GLU CB CG sing N N 82 GLU CB HB2 sing N N 83 GLU CB HB3 sing N N 84 GLU CG CD sing N N 85 GLU CG HG2 sing N N 86 GLU CG HG3 sing N N 87 GLU CD OE1 doub N N 88 GLU CD OE2 sing N N 89 GLU OE2 HE2 sing N N 90 GLU OXT HXT sing N N 91 GLY N CA sing N N 92 GLY N H sing N N 93 GLY N H2 sing N N 94 GLY CA C sing N N 95 GLY CA HA2 sing N N 96 GLY CA HA3 sing N N 97 GLY C O doub N N 98 GLY C OXT sing N N 99 GLY OXT HXT sing N N 100 HOH O H1 sing N N 101 HOH O H2 sing N N 102 ILE N CA sing N N 103 ILE N H sing N N 104 ILE N H2 sing N N 105 ILE CA C sing N N 106 ILE CA CB sing N N 107 ILE CA HA sing N N 108 ILE C O doub N N 109 ILE C OXT sing N N 110 ILE CB CG1 sing N N 111 ILE CB CG2 sing N N 112 ILE CB HB sing N N 113 ILE CG1 CD1 sing N N 114 ILE CG1 HG12 sing N N 115 ILE CG1 HG13 sing N N 116 ILE CG2 HG21 sing N N 117 ILE CG2 HG22 sing N N 118 ILE CG2 HG23 sing N N 119 ILE CD1 HD11 sing N N 120 ILE CD1 HD12 sing N N 121 ILE CD1 HD13 sing N N 122 ILE OXT HXT sing N N 123 LYS N CA sing N N 124 LYS N H sing N N 125 LYS N H2 sing N N 126 LYS CA C sing N N 127 LYS CA CB sing N N 128 LYS CA HA sing N N 129 LYS C O doub N N 130 LYS C OXT sing N N 131 LYS CB CG sing N N 132 LYS CB HB2 sing N N 133 LYS CB HB3 sing N N 134 LYS CG CD sing N N 135 LYS CG HG2 sing N N 136 LYS CG HG3 sing N N 137 LYS CD CE sing N N 138 LYS CD HD2 sing N N 139 LYS CD HD3 sing N N 140 LYS CE NZ sing N N 141 LYS CE HE2 sing N N 142 LYS CE HE3 sing N N 143 LYS NZ HZ1 sing N N 144 LYS NZ HZ2 sing N N 145 LYS NZ HZ3 sing N N 146 LYS OXT HXT sing N N 147 MET N CA sing N N 148 MET N H sing N N 149 MET N H2 sing N N 150 MET CA C sing N N 151 MET CA CB sing N N 152 MET CA HA sing N N 153 MET C O doub N N 154 MET C OXT sing N N 155 MET CB CG sing N N 156 MET CB HB2 sing N N 157 MET CB HB3 sing N N 158 MET CG SD sing N N 159 MET CG HG2 sing N N 160 MET CG HG3 sing N N 161 MET SD CE sing N N 162 MET CE HE1 sing N N 163 MET CE HE2 sing N N 164 MET CE HE3 sing N N 165 MET OXT HXT sing N N 166 PHE N CA sing N N 167 PHE N H sing N N 168 PHE N H2 sing N N 169 PHE CA C sing N N 170 PHE CA CB sing N N 171 PHE CA HA sing N N 172 PHE C O doub N N 173 PHE C OXT sing N N 174 PHE CB CG sing N N 175 PHE CB HB2 sing N N 176 PHE CB HB3 sing N N 177 PHE CG CD1 doub Y N 178 PHE CG CD2 sing Y N 179 PHE CD1 CE1 sing Y N 180 PHE CD1 HD1 sing N N 181 PHE CD2 CE2 doub Y N 182 PHE CD2 HD2 sing N N 183 PHE CE1 CZ doub Y N 184 PHE CE1 HE1 sing N N 185 PHE CE2 CZ sing Y N 186 PHE CE2 HE2 sing N N 187 PHE CZ HZ sing N N 188 PHE OXT HXT sing N N 189 PRO N CA sing N N 190 PRO N CD sing N N 191 PRO N H sing N N 192 PRO CA C sing N N 193 PRO CA CB sing N N 194 PRO CA HA sing N N 195 PRO C O doub N N 196 PRO C OXT sing N N 197 PRO CB CG sing N N 198 PRO CB HB2 sing N N 199 PRO CB HB3 sing N N 200 PRO CG CD sing N N 201 PRO CG HG2 sing N N 202 PRO CG HG3 sing N N 203 PRO CD HD2 sing N N 204 PRO CD HD3 sing N N 205 PRO OXT HXT sing N N 206 SO4 S O1 doub N N 207 SO4 S O2 doub N N 208 SO4 S O3 sing N N 209 SO4 S O4 sing N N 210 VAL N CA sing N N 211 VAL N H sing N N 212 VAL N H2 sing N N 213 VAL CA C sing N N 214 VAL CA CB sing N N 215 VAL CA HA sing N N 216 VAL C O doub N N 217 VAL C OXT sing N N 218 VAL CB CG1 sing N N 219 VAL CB CG2 sing N N 220 VAL CB HB sing N N 221 VAL CG1 HG11 sing N N 222 VAL CG1 HG12 sing N N 223 VAL CG1 HG13 sing N N 224 VAL CG2 HG21 sing N N 225 VAL CG2 HG22 sing N N 226 VAL CG2 HG23 sing N N 227 VAL OXT HXT sing N N 228 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan 18H01328 1 'Japan Society for the Promotion of Science (JSPS)' Japan 20K15854 2 'Japan Society for the Promotion of Science (JSPS)' Japan 22H01346 3 # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 CIT ? ? CIT ? ? 'SUBJECT OF INVESTIGATION' ? 2 SO4 ? ? SO4 ? ? 'SUBJECT OF INVESTIGATION' ? # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 8JVP _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 8JVQ _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.028558 _atom_sites.fract_transf_matrix[1][2] 0.016488 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032975 _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] 0.018295 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_