data_4YGT # _entry.id 4YGT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _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 4YGT pdb_00004ygt 10.2210/pdb4ygt/pdb WWPDB D_1000207343 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.details . _pdbx_database_related.db_id JCSG-418974 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4YGT _pdbx_database_status.recvd_initial_deposition_date 2015-02-26 _pdbx_database_status.SG_entry Y _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 ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To be published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystal structure of a DUF4309 family protein (YjgB) from Bacillus subtilis subsp. subtilis str. 168 at 2.13 A resolution' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 4YGT _cell.length_a 90.830 _cell.length_b 90.830 _cell.length_c 41.900 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YGT _symmetry.Int_Tables_number 169 _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # 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 'Uncharacterized protein YjgB' 17945.359 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 4 ? ? ? ? 4 water nat water 18.015 50 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'DUF4309 family protein' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;GAAQTNTLSENTNQSAAELVKNLYNTAYKGE(MSE)PQQAQGLTINKSTKGDVHAAFGEPERPVGGDNRFDLYHWN (MSE)GQPGYGFSYHKD(MSE)TISEIRYFGTGVERQLNLGGVTPEVLQKQLGPVNRVLTVPFTDEIDYVYDTGRYELHF VIGTDQTADHVNLKAK ; _entity_poly.pdbx_seq_one_letter_code_can ;GAAQTNTLSENTNQSAAELVKNLYNTAYKGEMPQQAQGLTINKSTKGDVHAAFGEPERPVGGDNRFDLYHWNMGQPGYGF SYHKDMTISEIRYFGTGVERQLNLGGVTPEVLQKQLGPVNRVLTVPFTDEIDYVYDTGRYELHFVIGTDQTADHVNLKAK ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-418974 # 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 ALA n 1 3 ALA n 1 4 GLN n 1 5 THR n 1 6 ASN n 1 7 THR n 1 8 LEU n 1 9 SER n 1 10 GLU n 1 11 ASN n 1 12 THR n 1 13 ASN n 1 14 GLN n 1 15 SER n 1 16 ALA n 1 17 ALA n 1 18 GLU n 1 19 LEU n 1 20 VAL n 1 21 LYS n 1 22 ASN n 1 23 LEU n 1 24 TYR n 1 25 ASN n 1 26 THR n 1 27 ALA n 1 28 TYR n 1 29 LYS n 1 30 GLY n 1 31 GLU n 1 32 MSE n 1 33 PRO n 1 34 GLN n 1 35 GLN n 1 36 ALA n 1 37 GLN n 1 38 GLY n 1 39 LEU n 1 40 THR n 1 41 ILE n 1 42 ASN n 1 43 LYS n 1 44 SER n 1 45 THR n 1 46 LYS n 1 47 GLY n 1 48 ASP n 1 49 VAL n 1 50 HIS n 1 51 ALA n 1 52 ALA n 1 53 PHE n 1 54 GLY n 1 55 GLU n 1 56 PRO n 1 57 GLU n 1 58 ARG n 1 59 PRO n 1 60 VAL n 1 61 GLY n 1 62 GLY n 1 63 ASP n 1 64 ASN n 1 65 ARG n 1 66 PHE n 1 67 ASP n 1 68 LEU n 1 69 TYR n 1 70 HIS n 1 71 TRP n 1 72 ASN n 1 73 MSE n 1 74 GLY n 1 75 GLN n 1 76 PRO n 1 77 GLY n 1 78 TYR n 1 79 GLY n 1 80 PHE n 1 81 SER n 1 82 TYR n 1 83 HIS n 1 84 LYS n 1 85 ASP n 1 86 MSE n 1 87 THR n 1 88 ILE n 1 89 SER n 1 90 GLU n 1 91 ILE n 1 92 ARG n 1 93 TYR n 1 94 PHE n 1 95 GLY n 1 96 THR n 1 97 GLY n 1 98 VAL n 1 99 GLU n 1 100 ARG n 1 101 GLN n 1 102 LEU n 1 103 ASN n 1 104 LEU n 1 105 GLY n 1 106 GLY n 1 107 VAL n 1 108 THR n 1 109 PRO n 1 110 GLU n 1 111 VAL n 1 112 LEU n 1 113 GLN n 1 114 LYS n 1 115 GLN n 1 116 LEU n 1 117 GLY n 1 118 PRO n 1 119 VAL n 1 120 ASN n 1 121 ARG n 1 122 VAL n 1 123 LEU n 1 124 THR n 1 125 VAL n 1 126 PRO n 1 127 PHE n 1 128 THR n 1 129 ASP n 1 130 GLU n 1 131 ILE n 1 132 ASP n 1 133 TYR n 1 134 VAL n 1 135 TYR n 1 136 ASP n 1 137 THR n 1 138 GLY n 1 139 ARG n 1 140 TYR n 1 141 GLU n 1 142 LEU n 1 143 HIS n 1 144 PHE n 1 145 VAL n 1 146 ILE n 1 147 GLY n 1 148 THR n 1 149 ASP n 1 150 GLN n 1 151 THR n 1 152 ALA n 1 153 ASP n 1 154 HIS n 1 155 VAL n 1 156 ASN n 1 157 LEU n 1 158 LYS n 1 159 ALA n 1 160 LYS 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 160 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'yjgB, BSU12150, NP_389097.1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 168 _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 'Bacillus subtilis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 224308 _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 PB1 _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 Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.db_code YJGB_BACSU _struct_ref.db_name UNP _struct_ref.details ? _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.seq_align ? _struct_ref.seq_dif ? _struct_ref.pdbx_db_accession O34960 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ;AAQTNTLSENTNQSAAELVKNLYNTAYKGEMPQQAQGLTINKSTKGDVHAAFGEPERPVGGDNRFDLYHWNMGQPGYGFS YHKDMTISEIRYFGTGVERQLNLGGVTPEVLQKQLGPVNRVLTVPFTDEIDYVYDTGRYELHFVIGTDQTADHVNLKAK ; _struct_ref.pdbx_align_begin 33 _struct_ref.pdbx_align_end ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4YGT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 160 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O34960 _struct_ref_seq.db_align_beg 33 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 191 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 33 _struct_ref_seq.pdbx_auth_seq_align_end 191 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4YGT _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code O34960 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 4YGT _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 2.78 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 55.73 _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, 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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.2M sodium sulfate, 20% polyethylene glycol 3350' _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_detector.details 'Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator' _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-07-28 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'double crystal Si(111)' _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 MAD _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9793 1.0 2 0.7514 1.0 3 0.9791 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 'SSRL BEAMLINE BL12-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9793,0.7514,0.9791 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL12-2 _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4YGT _reflns.d_resolution_high 2.13 _reflns.d_resolution_low 45.416 _reflns.pdbx_number_measured_all 120232 _reflns.number_obs 11231 _reflns.pdbx_Rmerge_I_obs 0.124 _reflns.pdbx_netI_over_sigmaI 14.580 _reflns.percent_possible_obs 99.900 _reflns.B_iso_Wilson_estimate 42.915 _reflns.Rmerge_F_obs 0.999 _reflns.observed_criterion_sigma_I -3.000 _reflns.pdbx_Rrim_I_all 0.130 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.130 2.210 11457 ? 1159 ? 1.635 1.9 ? ? ? ? ? 1161 ? ? 0.811 ? ? 99.800 1.726 ? ? 1 2.210 2.290 11210 ? 1004 ? 1.373 2.5 ? ? ? ? ? 1004 ? ? 0.885 ? ? 100.000 1.438 ? ? 2 2.290 2.400 13043 ? 1171 ? 1.163 2.8 ? ? ? ? ? 1171 ? ? 0.930 ? ? 100.000 1.219 ? ? 3 2.400 2.520 11751 ? 1067 ? 0.943 3.3 ? ? ? ? ? 1067 ? ? 0.870 ? ? 100.000 0.989 ? ? 4 2.520 2.680 12241 ? 1131 ? 0.583 5.2 ? ? ? ? ? 1131 ? ? 0.956 ? ? 100.000 0.612 ? ? 5 2.680 2.890 11342 ? 1122 ? 0.328 8.0 ? ? ? ? ? 1122 ? ? 0.980 ? ? 100.000 0.346 ? ? 6 2.890 3.180 12758 ? 1126 ? 0.205 12.9 ? ? ? ? ? 1126 ? ? 0.992 ? ? 100.000 0.215 ? ? 7 3.180 3.640 12493 ? 1134 ? 0.098 23.4 ? ? ? ? ? 1134 ? ? 0.998 ? ? 100.000 0.103 ? ? 8 3.640 4.570 11613 ? 1123 ? 0.052 36.8 ? ? ? ? ? 1128 ? ? 0.999 ? ? 99.600 0.054 ? ? 9 4.570 45.416 12324 ? 1181 ? 0.045 46.5 ? ? ? ? ? 1187 ? ? 0.999 ? ? 99.500 0.048 ? ? 10 # _refine.entry_id 4YGT _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 2.1300 _refine.ls_d_res_low 45.416 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8000 _refine.ls_number_reflns_obs 11202 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SULFATE FROM THE CRYSTALLIZATION CONDITIONS (SO4) AND 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1933 _refine.ls_R_factor_R_work 0.1913 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2313 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.7700 _refine.ls_number_reflns_R_free 534 _refine.ls_number_reflns_R_work 10668 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 62.4779 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -6.9609 _refine.aniso_B[2][2] -6.9609 _refine.aniso_B[3][3] 13.9219 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9438 _refine.correlation_coeff_Fo_to_Fc_free 0.9333 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 155.840 _refine.B_iso_min 28.970 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.750 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4YGT _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.Luzzati_coordinate_error_obs 0.398 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1169 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 21 _refine_hist.number_atoms_solvent 50 _refine_hist.number_atoms_total 1240 _refine_hist.d_res_high 2.1300 _refine_hist.d_res_low 45.416 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' t_dihedral_angle_d 542 ? ? 2.000 SINUSOIDAL 'X-RAY DIFFRACTION' t_trig_c_planes 36 ? ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_gen_planes 174 ? ? 5.000 HARMONIC 'X-RAY DIFFRACTION' t_it 1213 ? ? 20.000 HARMONIC 'X-RAY DIFFRACTION' t_nbd ? ? ? ? ? 'X-RAY DIFFRACTION' t_improper_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_pseud_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_chiral_improper_torsion 148 ? ? 5.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_sum_occupancies ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_distance ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_ideal_dist_contact 1414 ? ? 4.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_bond_d 1213 0.010 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_angle_deg 1638 1.150 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_omega_torsion ? 3.690 ? ? ? 'X-RAY DIFFRACTION' t_other_torsion ? 2.890 ? ? ? # _refine_ls_shell.d_res_high 2.1300 _refine_ls_shell.d_res_low 2.3300 _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.percent_reflns_obs 99.8000 _refine_ls_shell.number_reflns_R_work 2533 _refine_ls_shell.R_factor_all 0.2281 _refine_ls_shell.R_factor_R_work 0.2273 _refine_ls_shell.R_factor_R_free 0.2451 _refine_ls_shell.percent_reflns_R_free 4.4200 _refine_ls_shell.number_reflns_R_free 117 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 2650 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 4YGT _struct.title 'Crystal structure of a DUF4309 family protein (YjgB) from Bacillus subtilis subsp. subtilis str. 168 at 2.13 A resolution' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4YGT _struct_keywords.text ;putative secreted lipoprotein, the first structural representative of PF14172 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION, STRUCTURAL GENOMICS UNKNOWN FUNCTION ; _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS UNKNOWN FUNCTION' # 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 3 ? E N N 3 ? F N N 3 ? G N N 4 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 ASN A 13 ? TYR A 28 ? ASN A 44 TYR A 59 1 ? 16 HELX_P HELX_P2 AA2 PRO A 33 ? GLN A 37 ? PRO A 64 GLN A 68 5 ? 5 HELX_P HELX_P3 AA3 THR A 45 ? GLY A 54 ? THR A 76 GLY A 85 1 ? 10 HELX_P HELX_P4 AA4 GLU A 99 ? VAL A 107 ? GLU A 130 VAL A 138 5 ? 9 HELX_P HELX_P5 AA5 THR A 108 ? GLY A 117 ? THR A 139 GLY A 148 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GLU 31 C ? ? ? 1_555 A MSE 32 N ? ? A GLU 62 A MSE 63 1_555 ? ? ? ? ? ? ? 1.310 ? ? covale2 covale both ? A MSE 32 C ? ? ? 1_555 A PRO 33 N ? ? A MSE 63 A PRO 64 1_555 ? ? ? ? ? ? ? 1.352 ? ? covale3 covale both ? A ASN 72 C ? ? ? 1_555 A MSE 73 N ? ? A ASN 103 A MSE 104 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale4 covale both ? A MSE 73 C ? ? ? 1_555 A GLY 74 N ? ? A MSE 104 A GLY 105 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale5 covale both ? A ASP 85 C ? ? ? 1_555 A MSE 86 N ? ? A ASP 116 A MSE 117 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale6 covale both ? A MSE 86 C ? ? ? 1_555 A THR 87 N ? ? A MSE 117 A THR 118 1_555 ? ? ? ? ? ? ? 1.346 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 7 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA1 6 7 ? 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 ASP A 67 ? TYR A 69 ? ASP A 98 TYR A 100 AA1 2 GLY A 77 ? TYR A 82 ? GLY A 108 TYR A 113 AA1 3 ILE A 88 ? GLY A 95 ? ILE A 119 GLY A 126 AA1 4 ALA A 152 ? ALA A 159 ? ALA A 183 ALA A 190 AA1 5 TYR A 140 ? ILE A 146 ? TYR A 171 ILE A 177 AA1 6 ILE A 131 ? THR A 137 ? ILE A 162 THR A 168 AA1 7 ARG A 121 ? THR A 124 ? ARG A 152 THR A 155 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N TYR A 69 ? N TYR A 100 O TYR A 78 ? O TYR A 109 AA1 2 3 N GLY A 77 ? N GLY A 108 O PHE A 94 ? O PHE A 125 AA1 3 4 N ILE A 91 ? N ILE A 122 O LEU A 157 ? O LEU A 188 AA1 4 5 O ASN A 156 ? O ASN A 187 N HIS A 143 ? N HIS A 174 AA1 5 6 O ILE A 146 ? O ILE A 177 N ILE A 131 ? N ILE A 162 AA1 6 7 O VAL A 134 ? O VAL A 165 N ARG A 121 ? N ARG A 152 # 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 SO4 201 ? 6 'binding site for residue SO4 A 201' AC2 Software A EDO 202 ? 7 'binding site for residue EDO A 202' AC3 Software A EDO 203 ? 6 'binding site for residue EDO A 203' AC4 Software A EDO 204 ? 3 'binding site for residue EDO A 204' AC5 Software A EDO 205 ? 6 'binding site for residue EDO A 205' # 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 6 ARG A 65 ? ARG A 96 . ? 1_555 ? 2 AC1 6 HIS A 70 ? HIS A 101 . ? 2_655 ? 3 AC1 6 TRP A 71 ? TRP A 102 . ? 2_655 ? 4 AC1 6 ARG A 92 ? ARG A 123 . ? 1_555 ? 5 AC1 6 EDO D . ? EDO A 203 . ? 2_655 ? 6 AC1 6 HOH G . ? HOH A 313 . ? 1_555 ? 7 AC2 7 TYR A 69 ? TYR A 100 . ? 1_555 ? 8 AC2 7 HIS A 70 ? HIS A 101 . ? 1_555 ? 9 AC2 7 ASN A 72 ? ASN A 103 . ? 1_555 ? 10 AC2 7 GLN A 75 ? GLN A 106 . ? 1_555 ? 11 AC2 7 PRO A 76 ? PRO A 107 . ? 1_555 ? 12 AC2 7 HOH G . ? HOH A 335 . ? 1_555 ? 13 AC2 7 HOH G . ? HOH A 336 . ? 1_555 ? 14 AC3 6 ASP A 63 ? ASP A 94 . ? 3_664 ? 15 AC3 6 TRP A 71 ? TRP A 102 . ? 1_555 ? 16 AC3 6 MSE A 73 ? MSE A 104 . ? 1_555 ? 17 AC3 6 GLY A 97 ? GLY A 128 . ? 1_555 ? 18 AC3 6 VAL A 98 ? VAL A 129 . ? 1_555 ? 19 AC3 6 SO4 B . ? SO4 A 201 . ? 3_664 ? 20 AC4 3 ASN A 25 ? ASN A 56 . ? 1_555 ? 21 AC4 3 GLY A 47 ? GLY A 78 . ? 4_665 ? 22 AC4 3 ASP A 48 ? ASP A 79 . ? 4_665 ? 23 AC5 6 TYR A 28 ? TYR A 59 . ? 1_555 ? 24 AC5 6 LYS A 29 ? LYS A 60 . ? 1_555 ? 25 AC5 6 GLN A 35 ? GLN A 66 . ? 4_665 ? 26 AC5 6 ALA A 52 ? ALA A 83 . ? 4_665 ? 27 AC5 6 ARG A 139 ? ARG A 170 . ? 1_555 ? 28 AC5 6 TYR A 140 ? TYR A 171 . ? 1_555 ? # _atom_sites.entry_id 4YGT _atom_sites.fract_transf_matrix[1][1] 0.011010 _atom_sites.fract_transf_matrix[1][2] 0.006356 _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] 0.012713 _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] 0.023866 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S SE # 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 0 ? ? ? A . n A 1 2 ALA 2 33 ? ? ? A . n A 1 3 ALA 3 34 ? ? ? A . n A 1 4 GLN 4 35 ? ? ? A . n A 1 5 THR 5 36 ? ? ? A . n A 1 6 ASN 6 37 ? ? ? A . n A 1 7 THR 7 38 ? ? ? A . n A 1 8 LEU 8 39 ? ? ? A . n A 1 9 SER 9 40 ? ? ? A . n A 1 10 GLU 10 41 ? ? ? A . n A 1 11 ASN 11 42 ? ? ? A . n A 1 12 THR 12 43 ? ? ? A . n A 1 13 ASN 13 44 44 ASN ASN A . n A 1 14 GLN 14 45 45 GLN GLN A . n A 1 15 SER 15 46 46 SER SER A . n A 1 16 ALA 16 47 47 ALA ALA A . n A 1 17 ALA 17 48 48 ALA ALA A . n A 1 18 GLU 18 49 49 GLU GLU A . n A 1 19 LEU 19 50 50 LEU LEU A . n A 1 20 VAL 20 51 51 VAL VAL A . n A 1 21 LYS 21 52 52 LYS LYS A . n A 1 22 ASN 22 53 53 ASN ASN A . n A 1 23 LEU 23 54 54 LEU LEU A . n A 1 24 TYR 24 55 55 TYR TYR A . n A 1 25 ASN 25 56 56 ASN ASN A . n A 1 26 THR 26 57 57 THR THR A . n A 1 27 ALA 27 58 58 ALA ALA A . n A 1 28 TYR 28 59 59 TYR TYR A . n A 1 29 LYS 29 60 60 LYS LYS A . n A 1 30 GLY 30 61 61 GLY GLY A . n A 1 31 GLU 31 62 62 GLU GLU A . n A 1 32 MSE 32 63 63 MSE MSE A . n A 1 33 PRO 33 64 64 PRO PRO A . n A 1 34 GLN 34 65 65 GLN GLN A . n A 1 35 GLN 35 66 66 GLN GLN A . n A 1 36 ALA 36 67 67 ALA ALA A . n A 1 37 GLN 37 68 68 GLN GLN A . n A 1 38 GLY 38 69 69 GLY GLY A . n A 1 39 LEU 39 70 70 LEU LEU A . n A 1 40 THR 40 71 71 THR THR A . n A 1 41 ILE 41 72 72 ILE ILE A . n A 1 42 ASN 42 73 73 ASN ASN A . n A 1 43 LYS 43 74 74 LYS LYS A . n A 1 44 SER 44 75 75 SER SER A . n A 1 45 THR 45 76 76 THR THR A . n A 1 46 LYS 46 77 77 LYS LYS A . n A 1 47 GLY 47 78 78 GLY GLY A . n A 1 48 ASP 48 79 79 ASP ASP A . n A 1 49 VAL 49 80 80 VAL VAL A . n A 1 50 HIS 50 81 81 HIS HIS A . n A 1 51 ALA 51 82 82 ALA ALA A . n A 1 52 ALA 52 83 83 ALA ALA A . n A 1 53 PHE 53 84 84 PHE PHE A . n A 1 54 GLY 54 85 85 GLY GLY A . n A 1 55 GLU 55 86 86 GLU GLU A . n A 1 56 PRO 56 87 87 PRO PRO A . n A 1 57 GLU 57 88 88 GLU GLU A . n A 1 58 ARG 58 89 89 ARG ARG A . n A 1 59 PRO 59 90 90 PRO PRO A . n A 1 60 VAL 60 91 91 VAL VAL A . n A 1 61 GLY 61 92 92 GLY GLY A . n A 1 62 GLY 62 93 93 GLY GLY A . n A 1 63 ASP 63 94 94 ASP ASP A . n A 1 64 ASN 64 95 95 ASN ASN A . n A 1 65 ARG 65 96 96 ARG ARG A . n A 1 66 PHE 66 97 97 PHE PHE A . n A 1 67 ASP 67 98 98 ASP ASP A . n A 1 68 LEU 68 99 99 LEU LEU A . n A 1 69 TYR 69 100 100 TYR TYR A . n A 1 70 HIS 70 101 101 HIS HIS A . n A 1 71 TRP 71 102 102 TRP TRP A . n A 1 72 ASN 72 103 103 ASN ASN A . n A 1 73 MSE 73 104 104 MSE MSE A . n A 1 74 GLY 74 105 105 GLY GLY A . n A 1 75 GLN 75 106 106 GLN GLN A . n A 1 76 PRO 76 107 107 PRO PRO A . n A 1 77 GLY 77 108 108 GLY GLY A . n A 1 78 TYR 78 109 109 TYR TYR A . n A 1 79 GLY 79 110 110 GLY GLY A . n A 1 80 PHE 80 111 111 PHE PHE A . n A 1 81 SER 81 112 112 SER SER A . n A 1 82 TYR 82 113 113 TYR TYR A . n A 1 83 HIS 83 114 114 HIS HIS A . n A 1 84 LYS 84 115 115 LYS LYS A . n A 1 85 ASP 85 116 116 ASP ASP A . n A 1 86 MSE 86 117 117 MSE MSE A . n A 1 87 THR 87 118 118 THR THR A . n A 1 88 ILE 88 119 119 ILE ILE A . n A 1 89 SER 89 120 120 SER SER A . n A 1 90 GLU 90 121 121 GLU GLU A . n A 1 91 ILE 91 122 122 ILE ILE A . n A 1 92 ARG 92 123 123 ARG ARG A . n A 1 93 TYR 93 124 124 TYR TYR A . n A 1 94 PHE 94 125 125 PHE PHE A . n A 1 95 GLY 95 126 126 GLY GLY A . n A 1 96 THR 96 127 127 THR THR A . n A 1 97 GLY 97 128 128 GLY GLY A . n A 1 98 VAL 98 129 129 VAL VAL A . n A 1 99 GLU 99 130 130 GLU GLU A . n A 1 100 ARG 100 131 131 ARG ARG A . n A 1 101 GLN 101 132 132 GLN GLN A . n A 1 102 LEU 102 133 133 LEU LEU A . n A 1 103 ASN 103 134 134 ASN ASN A . n A 1 104 LEU 104 135 135 LEU LEU A . n A 1 105 GLY 105 136 136 GLY GLY A . n A 1 106 GLY 106 137 137 GLY GLY A . n A 1 107 VAL 107 138 138 VAL VAL A . n A 1 108 THR 108 139 139 THR THR A . n A 1 109 PRO 109 140 140 PRO PRO A . n A 1 110 GLU 110 141 141 GLU GLU A . n A 1 111 VAL 111 142 142 VAL VAL A . n A 1 112 LEU 112 143 143 LEU LEU A . n A 1 113 GLN 113 144 144 GLN GLN A . n A 1 114 LYS 114 145 145 LYS LYS A . n A 1 115 GLN 115 146 146 GLN GLN A . n A 1 116 LEU 116 147 147 LEU LEU A . n A 1 117 GLY 117 148 148 GLY GLY A . n A 1 118 PRO 118 149 149 PRO PRO A . n A 1 119 VAL 119 150 150 VAL VAL A . n A 1 120 ASN 120 151 151 ASN ASN A . n A 1 121 ARG 121 152 152 ARG ARG A . n A 1 122 VAL 122 153 153 VAL VAL A . n A 1 123 LEU 123 154 154 LEU LEU A . n A 1 124 THR 124 155 155 THR THR A . n A 1 125 VAL 125 156 156 VAL VAL A . n A 1 126 PRO 126 157 157 PRO PRO A . n A 1 127 PHE 127 158 158 PHE PHE A . n A 1 128 THR 128 159 159 THR THR A . n A 1 129 ASP 129 160 160 ASP ASP A . n A 1 130 GLU 130 161 161 GLU GLU A . n A 1 131 ILE 131 162 162 ILE ILE A . n A 1 132 ASP 132 163 163 ASP ASP A . n A 1 133 TYR 133 164 164 TYR TYR A . n A 1 134 VAL 134 165 165 VAL VAL A . n A 1 135 TYR 135 166 166 TYR TYR A . n A 1 136 ASP 136 167 167 ASP ASP A . n A 1 137 THR 137 168 168 THR THR A . n A 1 138 GLY 138 169 169 GLY GLY A . n A 1 139 ARG 139 170 170 ARG ARG A . n A 1 140 TYR 140 171 171 TYR TYR A . n A 1 141 GLU 141 172 172 GLU GLU A . n A 1 142 LEU 142 173 173 LEU LEU A . n A 1 143 HIS 143 174 174 HIS HIS A . n A 1 144 PHE 144 175 175 PHE PHE A . n A 1 145 VAL 145 176 176 VAL VAL A . n A 1 146 ILE 146 177 177 ILE ILE A . n A 1 147 GLY 147 178 178 GLY GLY A . n A 1 148 THR 148 179 179 THR THR A . n A 1 149 ASP 149 180 180 ASP ASP A . n A 1 150 GLN 150 181 181 GLN GLN A . n A 1 151 THR 151 182 182 THR THR A . n A 1 152 ALA 152 183 183 ALA ALA A . n A 1 153 ASP 153 184 184 ASP ASP A . n A 1 154 HIS 154 185 185 HIS HIS A . n A 1 155 VAL 155 186 186 VAL VAL A . n A 1 156 ASN 156 187 187 ASN ASN A . n A 1 157 LEU 157 188 188 LEU LEU A . n A 1 158 LYS 158 189 189 LYS LYS A . n A 1 159 ALA 159 190 190 ALA ALA A . n A 1 160 LYS 160 191 191 LYS LYS A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.initial_of_center JCSG # 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 1 201 192 SO4 SO4 A . C 3 EDO 1 202 193 EDO EDO A . D 3 EDO 1 203 194 EDO EDO A . E 3 EDO 1 204 195 EDO EDO A . F 3 EDO 1 205 196 EDO EDO A . G 4 HOH 1 301 200 HOH HOH A . G 4 HOH 2 302 246 HOH HOH A . G 4 HOH 3 303 225 HOH HOH A . G 4 HOH 4 304 233 HOH HOH A . G 4 HOH 5 305 217 HOH HOH A . G 4 HOH 6 306 205 HOH HOH A . G 4 HOH 7 307 203 HOH HOH A . G 4 HOH 8 308 207 HOH HOH A . G 4 HOH 9 309 235 HOH HOH A . G 4 HOH 10 310 242 HOH HOH A . G 4 HOH 11 311 218 HOH HOH A . G 4 HOH 12 312 201 HOH HOH A . G 4 HOH 13 313 240 HOH HOH A . G 4 HOH 14 314 230 HOH HOH A . G 4 HOH 15 315 206 HOH HOH A . G 4 HOH 16 316 237 HOH HOH A . G 4 HOH 17 317 214 HOH HOH A . G 4 HOH 18 318 211 HOH HOH A . G 4 HOH 19 319 202 HOH HOH A . G 4 HOH 20 320 239 HOH HOH A . G 4 HOH 21 321 245 HOH HOH A . G 4 HOH 22 322 234 HOH HOH A . G 4 HOH 23 323 228 HOH HOH A . G 4 HOH 24 324 229 HOH HOH A . G 4 HOH 25 325 236 HOH HOH A . G 4 HOH 26 326 197 HOH HOH A . G 4 HOH 27 327 198 HOH HOH A . G 4 HOH 28 328 199 HOH HOH A . G 4 HOH 29 329 204 HOH HOH A . G 4 HOH 30 330 208 HOH HOH A . G 4 HOH 31 331 209 HOH HOH A . G 4 HOH 32 332 210 HOH HOH A . G 4 HOH 33 333 212 HOH HOH A . G 4 HOH 34 334 213 HOH HOH A . G 4 HOH 35 335 215 HOH HOH A . G 4 HOH 36 336 216 HOH HOH A . G 4 HOH 37 337 219 HOH HOH A . G 4 HOH 38 338 220 HOH HOH A . G 4 HOH 39 339 221 HOH HOH A . G 4 HOH 40 340 222 HOH HOH A . G 4 HOH 41 341 223 HOH HOH A . G 4 HOH 42 342 224 HOH HOH A . G 4 HOH 43 343 226 HOH HOH A . G 4 HOH 44 344 227 HOH HOH A . G 4 HOH 45 345 231 HOH HOH A . G 4 HOH 46 346 232 HOH HOH A . G 4 HOH 47 347 238 HOH HOH A . G 4 HOH 48 348 241 HOH HOH A . G 4 HOH 49 349 243 HOH HOH A . G 4 HOH 50 350 244 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 32 A MSE 63 ? MET 'modified residue' 2 A MSE 73 A MSE 104 ? MET 'modified residue' 3 A MSE 86 A MSE 117 ? MET 'modified residue' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2015-03-18 2 'Structure model' 1 1 2017-11-22 3 'Structure model' 1 2 2018-01-24 4 'Structure model' 1 3 2023-02-01 # _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' 'Derived calculations' 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Source and taxonomy' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' entity_src_gen 2 2 'Structure model' pdbx_struct_oper_list 3 2 'Structure model' software 4 3 'Structure model' citation_author 5 4 'Structure model' database_2 6 4 'Structure model' struct_ref_seq_dif # 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' '_entity_src_gen.pdbx_alt_source_flag' 2 2 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 3 3 'Structure model' '_citation_author.name' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_struct_ref_seq_dif.details' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 34.7307 _pdbx_refine_tls.origin_y 35.9897 _pdbx_refine_tls.origin_z 27.7195 _pdbx_refine_tls.T[1][1] -0.2169 _pdbx_refine_tls.T[2][2] -0.0107 _pdbx_refine_tls.T[3][3] -0.2413 _pdbx_refine_tls.T[1][2] 0.1254 _pdbx_refine_tls.T[1][3] -0.0046 _pdbx_refine_tls.T[2][3] 0.0148 _pdbx_refine_tls.L[1][1] 5.1656 _pdbx_refine_tls.L[2][2] 4.8526 _pdbx_refine_tls.L[3][3] 6.4912 _pdbx_refine_tls.L[1][2] -3.9082 _pdbx_refine_tls.L[1][3] -0.7098 _pdbx_refine_tls.L[2][3] 1.8697 _pdbx_refine_tls.S[1][1] -0.2098 _pdbx_refine_tls.S[2][2] 0.4187 _pdbx_refine_tls.S[3][3] -0.2089 _pdbx_refine_tls.S[1][2] -0.4713 _pdbx_refine_tls.S[1][3] 0.1111 _pdbx_refine_tls.S[2][3] -0.3952 _pdbx_refine_tls.S[2][1] 0.2057 _pdbx_refine_tls.S[3][1] -0.0039 _pdbx_refine_tls.S[3][2] 0.6262 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 44 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 191 _pdbx_refine_tls_group.selection_details '{A|44 - 191}' _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? # _phasing.method MAD # 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 extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.10 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELX ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHARP ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? 'January 10, 2014 BUILT=20140307' 4 ? refinement ? ? ? ? ? ? ? ? ? ? ? BUSTER ? ? ? 2.10.2 5 # _pdbx_entry_details.entry_id 4YGT _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT (RESIDUES 33-191) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLN A 65 ? ? 60.56 -116.41 2 1 LYS A 74 ? ? -129.89 -54.87 3 1 ARG A 89 ? ? -165.38 102.54 4 1 MSE A 104 ? ? 53.87 -127.53 5 1 ASN A 134 ? ? -134.82 -124.01 6 1 GLN A 181 ? ? -78.68 39.79 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GLN 132 ? CG ? A GLN 101 CG 2 1 Y 1 A GLN 132 ? CD ? A GLN 101 CD 3 1 Y 1 A GLN 132 ? OE1 ? A GLN 101 OE1 4 1 Y 1 A GLN 132 ? NE2 ? A GLN 101 NE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A ALA 33 ? A ALA 2 3 1 Y 1 A ALA 34 ? A ALA 3 4 1 Y 1 A GLN 35 ? A GLN 4 5 1 Y 1 A THR 36 ? A THR 5 6 1 Y 1 A ASN 37 ? A ASN 6 7 1 Y 1 A THR 38 ? A THR 7 8 1 Y 1 A LEU 39 ? A LEU 8 9 1 Y 1 A SER 40 ? A SER 9 10 1 Y 1 A GLU 41 ? A GLU 10 11 1 Y 1 A ASN 42 ? A ASN 11 12 1 Y 1 A THR 43 ? A THR 12 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 1,2-ETHANEDIOL EDO 4 water HOH #