data_6IXE # _entry.id 6IXE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.303 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6IXE WWPDB D_1300010107 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6IXE _pdbx_database_status.recvd_initial_deposition_date 2018-12-10 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Goto-Ito, S.' 1 0000-0003-4108-1348 'Yamagata, A.' 2 ? 'Sato, Y.' 3 ? 'Fukai, S.' 4 0000-0002-1241-1443 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Life Sci Alliance' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2575-1077 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 2 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.26508/lsa.201900297 _citation.pdbx_database_id_PubMed 30872413 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Goto-Ito, S.' 1 ? primary 'Morooka, N.' 2 ? primary 'Yamagata, A.' 3 ? primary 'Sato, Y.' 4 ? primary 'Sato, K.' 5 0000-0002-1034-5091 primary 'Fukai, S.' 6 0000-0002-1241-1443 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 6IXE _cell.details ? _cell.formula_units_Z ? _cell.length_a 79.250 _cell.length_a_esd ? _cell.length_b 79.250 _cell.length_b_esd ? _cell.length_c 108.076 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IXE _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'SH3 domain-binding protein 5' 26690.434 1 ? M167A,R260A,R261A,R262A ? ? 2 non-polymer syn 'SUCCINIC ACID' 118.088 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'SH3BP-5,SH3 domain-binding protein that preferentially associates with BTK' # _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 ;SHVDPRIQGELEKLNQSTDDINRRETELEDARQKFRSVLVEATVKLDELVKKIGKAVEDSKPYWEARRVARQAQLEAQKA TQDFQRATEVLRAAKETISLAEQRLLEDDKRQFDSAWQE(MSE)LNHATQRVAEAEQTKTRSELVHKETAARYNAA (MSE)GR(MSE)RQLEKKLKRAINKSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLAKGEYK(MSE)ALKNLE(MSE)IS DEIHEAAASSA(MSE) ; _entity_poly.pdbx_seq_one_letter_code_can ;SHVDPRIQGELEKLNQSTDDINRRETELEDARQKFRSVLVEATVKLDELVKKIGKAVEDSKPYWEARRVARQAQLEAQKA TQDFQRATEVLRAAKETISLAEQRLLEDDKRQFDSAWQEMLNHATQRVAEAEQTKTRSELVHKETAARYNAAMGRMRQLE KKLKRAINKSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLAKGEYKMALKNLEMISDEIHEAAASSAM ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 HIS n 1 3 VAL n 1 4 ASP n 1 5 PRO n 1 6 ARG n 1 7 ILE n 1 8 GLN n 1 9 GLY n 1 10 GLU n 1 11 LEU n 1 12 GLU n 1 13 LYS n 1 14 LEU n 1 15 ASN n 1 16 GLN n 1 17 SER n 1 18 THR n 1 19 ASP n 1 20 ASP n 1 21 ILE n 1 22 ASN n 1 23 ARG n 1 24 ARG n 1 25 GLU n 1 26 THR n 1 27 GLU n 1 28 LEU n 1 29 GLU n 1 30 ASP n 1 31 ALA n 1 32 ARG n 1 33 GLN n 1 34 LYS n 1 35 PHE n 1 36 ARG n 1 37 SER n 1 38 VAL n 1 39 LEU n 1 40 VAL n 1 41 GLU n 1 42 ALA n 1 43 THR n 1 44 VAL n 1 45 LYS n 1 46 LEU n 1 47 ASP n 1 48 GLU n 1 49 LEU n 1 50 VAL n 1 51 LYS n 1 52 LYS n 1 53 ILE n 1 54 GLY n 1 55 LYS n 1 56 ALA n 1 57 VAL n 1 58 GLU n 1 59 ASP n 1 60 SER n 1 61 LYS n 1 62 PRO n 1 63 TYR n 1 64 TRP n 1 65 GLU n 1 66 ALA n 1 67 ARG n 1 68 ARG n 1 69 VAL n 1 70 ALA n 1 71 ARG n 1 72 GLN n 1 73 ALA n 1 74 GLN n 1 75 LEU n 1 76 GLU n 1 77 ALA n 1 78 GLN n 1 79 LYS n 1 80 ALA n 1 81 THR n 1 82 GLN n 1 83 ASP n 1 84 PHE n 1 85 GLN n 1 86 ARG n 1 87 ALA n 1 88 THR n 1 89 GLU n 1 90 VAL n 1 91 LEU n 1 92 ARG n 1 93 ALA n 1 94 ALA n 1 95 LYS n 1 96 GLU n 1 97 THR n 1 98 ILE n 1 99 SER n 1 100 LEU n 1 101 ALA n 1 102 GLU n 1 103 GLN n 1 104 ARG n 1 105 LEU n 1 106 LEU n 1 107 GLU n 1 108 ASP n 1 109 ASP n 1 110 LYS n 1 111 ARG n 1 112 GLN n 1 113 PHE n 1 114 ASP n 1 115 SER n 1 116 ALA n 1 117 TRP n 1 118 GLN n 1 119 GLU n 1 120 MSE n 1 121 LEU n 1 122 ASN n 1 123 HIS n 1 124 ALA n 1 125 THR n 1 126 GLN n 1 127 ARG n 1 128 VAL n 1 129 ALA n 1 130 GLU n 1 131 ALA n 1 132 GLU n 1 133 GLN n 1 134 THR n 1 135 LYS n 1 136 THR n 1 137 ARG n 1 138 SER n 1 139 GLU n 1 140 LEU n 1 141 VAL n 1 142 HIS n 1 143 LYS n 1 144 GLU n 1 145 THR n 1 146 ALA n 1 147 ALA n 1 148 ARG n 1 149 TYR n 1 150 ASN n 1 151 ALA n 1 152 ALA n 1 153 MSE n 1 154 GLY n 1 155 ARG n 1 156 MSE n 1 157 ARG n 1 158 GLN n 1 159 LEU n 1 160 GLU n 1 161 LYS n 1 162 LYS n 1 163 LEU n 1 164 LYS n 1 165 ARG n 1 166 ALA n 1 167 ILE n 1 168 ASN n 1 169 LYS n 1 170 SER n 1 171 LYS n 1 172 PRO n 1 173 TYR n 1 174 PHE n 1 175 GLU n 1 176 LEU n 1 177 LYS n 1 178 ALA n 1 179 LYS n 1 180 TYR n 1 181 TYR n 1 182 VAL n 1 183 GLN n 1 184 LEU n 1 185 GLU n 1 186 GLN n 1 187 LEU n 1 188 LYS n 1 189 LYS n 1 190 THR n 1 191 VAL n 1 192 ASP n 1 193 ASP n 1 194 LEU n 1 195 GLN n 1 196 ALA n 1 197 LYS n 1 198 LEU n 1 199 THR n 1 200 LEU n 1 201 ALA n 1 202 LYS n 1 203 GLY n 1 204 GLU n 1 205 TYR n 1 206 LYS n 1 207 MSE n 1 208 ALA n 1 209 LEU n 1 210 LYS n 1 211 ASN n 1 212 LEU n 1 213 GLU n 1 214 MSE n 1 215 ILE n 1 216 SER n 1 217 ASP n 1 218 GLU n 1 219 ILE n 1 220 HIS n 1 221 GLU n 1 222 ALA n 1 223 ALA n 1 224 ALA n 1 225 SER n 1 226 SER n 1 227 ALA n 1 228 MSE 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 228 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'SH3BP5, SAB' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 ? _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code 3BP5_HUMAN _struct_ref.pdbx_db_accession O60239 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VDPRIQGELEKLNQSTDDINRRETELEDARQKFRSVLVEATVKLDELVKKIGKAVEDSKPYWEARRVARQAQLEAQKATQ DFQRATEVLRAAKETISLAEQRLLEDDKRQFDSAWQEMLNHATQRVMEAEQTKTRSELVHKETAARYNAAMGRMRQLEKK LKRAINKSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLAKGEYKMALKNLEMISDEIHERRRSSAM ; _struct_ref.pdbx_align_begin 41 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6IXE _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 228 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O60239 _struct_ref_seq.db_align_beg 41 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 266 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 41 _struct_ref_seq.pdbx_auth_seq_align_end 266 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 6IXE SER A 1 ? UNP O60239 ? ? 'expression tag' 39 1 1 6IXE HIS A 2 ? UNP O60239 ? ? 'expression tag' 40 2 1 6IXE ALA A 129 ? UNP O60239 MET 167 'engineered mutation' 167 3 1 6IXE ALA A 222 ? UNP O60239 ARG 260 'engineered mutation' 260 4 1 6IXE ALA A 223 ? UNP O60239 ARG 261 'engineered mutation' 261 5 1 6IXE ALA A 224 ? UNP O60239 ARG 262 'engineered mutation' 262 6 # 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 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 SIN non-polymer . 'SUCCINIC ACID' ? 'C4 H6 O4' 118.088 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 6IXE _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 3.18 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 61.29 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.1M succinic acid (pH 7.0), 12% PEG 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.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2018-01-29 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _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 BL41XU' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9792 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL41XU _diffrn_source.pdbx_synchrotron_site SPring-8 # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6IXE _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.35 _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 4777 _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 96.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value 0.158 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 30 _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 ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 3.35 _reflns_shell.d_res_low 3.41 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all ? _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value 0.357 _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 ? _reflns_shell.pdbx_R_split ? # _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 6IXE _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 3.350 _refine.ls_d_res_low 38.899 _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 4689 _refine.ls_number_reflns_R_free 239 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.90 _refine.ls_percent_reflns_R_free 5.10 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2714 _refine.ls_R_factor_R_free 0.3138 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2691 _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.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 1.60 _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 SAD _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 42.51 _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 0.65 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1737 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1745 _refine_hist.d_res_high 3.350 _refine_hist.d_res_low 38.899 # 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' ? 0.003 ? 1762 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.658 ? 2357 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 11.417 ? 702 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.019 ? 262 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.002 ? 306 ? 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 _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_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 3.3505 4.2204 . . 117 2162 95.00 . . . 0.3859 . 0.3548 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.2204 38.9011 . . 122 2288 99.00 . . . 0.2853 . 0.2398 . . . . . . . . . . # _struct.entry_id 6IXE _struct.title 'Crystal structure of SeMet apo SH3BP5 (I41)' _struct.pdbx_descriptor 'SH3 domain-binding protein 5' _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 6IXE _struct_keywords.text 'Rab11, GEF, SH3BP5, SIGNALING PROTEIN' _struct_keywords.pdbx_keywords 'SIGNALING 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 ? # 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 VAL A 3 ? ILE A 53 ? VAL A 41 ILE A 91 1 ? 51 HELX_P HELX_P2 AA2 ILE A 53 ? LEU A 105 ? ILE A 91 LEU A 143 1 ? 53 HELX_P HELX_P3 AA3 ASP A 114 ? LYS A 162 ? ASP A 152 LYS A 200 1 ? 49 HELX_P HELX_P4 AA4 ALA A 166 ? ALA A 222 ? ALA A 204 ALA A 260 1 ? 57 # _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 covale1 covale both ? A GLU 119 C ? ? ? 1_555 A MSE 120 N ? ? A GLU 157 A MSE 158 1_555 ? ? ? ? ? ? ? 1.329 ? covale2 covale both ? A MSE 120 C ? ? ? 1_555 A LEU 121 N ? ? A MSE 158 A LEU 159 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale both ? A ALA 152 C ? ? ? 1_555 A MSE 153 N ? ? A ALA 190 A MSE 191 1_555 ? ? ? ? ? ? ? 1.332 ? covale4 covale both ? A MSE 153 C ? ? ? 1_555 A GLY 154 N ? ? A MSE 191 A GLY 192 1_555 ? ? ? ? ? ? ? 1.329 ? covale5 covale both ? A ARG 155 C ? ? ? 1_555 A MSE 156 N ? ? A ARG 193 A MSE 194 1_555 ? ? ? ? ? ? ? 1.329 ? covale6 covale both ? A MSE 156 C ? ? ? 1_555 A ARG 157 N ? ? A MSE 194 A ARG 195 1_555 ? ? ? ? ? ? ? 1.329 ? covale7 covale both ? A LYS 206 C ? ? ? 1_555 A MSE 207 N ? ? A LYS 244 A MSE 245 1_555 ? ? ? ? ? ? ? 1.331 ? covale8 covale both ? A MSE 207 C ? ? ? 1_555 A ALA 208 N ? ? A MSE 245 A ALA 246 1_555 ? ? ? ? ? ? ? 1.329 ? covale9 covale both ? A GLU 213 C ? ? ? 1_555 A MSE 214 N ? ? A GLU 251 A MSE 252 1_555 ? ? ? ? ? ? ? 1.329 ? covale10 covale both ? A MSE 214 C ? ? ? 1_555 A ILE 215 N ? ? A MSE 252 A ILE 253 1_555 ? ? ? ? ? ? ? 1.330 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id SIN _struct_site.pdbx_auth_seq_id 301 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 3 _struct_site.details 'binding site for residue SIN A 301' # 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 3 ASN A 15 ? ASN A 53 . ? 1_555 ? 2 AC1 3 GLN A 16 ? GLN A 54 . ? 1_555 ? 3 AC1 3 ASP A 19 ? ASP A 57 . ? 1_555 ? # _atom_sites.entry_id 6IXE _atom_sites.fract_transf_matrix[1][1] 0.012618 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.012618 _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] 0.009253 _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 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 SER 1 39 ? ? ? A . n A 1 2 HIS 2 40 ? ? ? A . n A 1 3 VAL 3 41 41 VAL VAL A . n A 1 4 ASP 4 42 42 ASP ASP A . n A 1 5 PRO 5 43 43 PRO PRO A . n A 1 6 ARG 6 44 44 ARG ARG A . n A 1 7 ILE 7 45 45 ILE ILE A . n A 1 8 GLN 8 46 46 GLN GLN A . n A 1 9 GLY 9 47 47 GLY GLY A . n A 1 10 GLU 10 48 48 GLU GLU A . n A 1 11 LEU 11 49 49 LEU LEU A . n A 1 12 GLU 12 50 50 GLU GLU A . n A 1 13 LYS 13 51 51 LYS LYS A . n A 1 14 LEU 14 52 52 LEU LEU A . n A 1 15 ASN 15 53 53 ASN ASN A . n A 1 16 GLN 16 54 54 GLN GLN A . n A 1 17 SER 17 55 55 SER SER A . n A 1 18 THR 18 56 56 THR THR A . n A 1 19 ASP 19 57 57 ASP ASP A . n A 1 20 ASP 20 58 58 ASP ASP A . n A 1 21 ILE 21 59 59 ILE ILE A . n A 1 22 ASN 22 60 60 ASN ASN A . n A 1 23 ARG 23 61 61 ARG ARG A . n A 1 24 ARG 24 62 62 ARG ARG A . n A 1 25 GLU 25 63 63 GLU GLU A . n A 1 26 THR 26 64 64 THR THR A . n A 1 27 GLU 27 65 65 GLU GLU A . n A 1 28 LEU 28 66 66 LEU LEU A . n A 1 29 GLU 29 67 67 GLU GLU A . n A 1 30 ASP 30 68 68 ASP ASP A . n A 1 31 ALA 31 69 69 ALA ALA A . n A 1 32 ARG 32 70 70 ARG ARG A . n A 1 33 GLN 33 71 71 GLN GLN A . n A 1 34 LYS 34 72 72 LYS LYS A . n A 1 35 PHE 35 73 73 PHE PHE A . n A 1 36 ARG 36 74 74 ARG ARG A . n A 1 37 SER 37 75 75 SER SER A . n A 1 38 VAL 38 76 76 VAL VAL A . n A 1 39 LEU 39 77 77 LEU LEU A . n A 1 40 VAL 40 78 78 VAL VAL A . n A 1 41 GLU 41 79 79 GLU GLU A . n A 1 42 ALA 42 80 80 ALA ALA A . n A 1 43 THR 43 81 81 THR THR A . n A 1 44 VAL 44 82 82 VAL VAL A . n A 1 45 LYS 45 83 83 LYS LYS A . n A 1 46 LEU 46 84 84 LEU LEU A . n A 1 47 ASP 47 85 85 ASP ASP A . n A 1 48 GLU 48 86 86 GLU GLU A . n A 1 49 LEU 49 87 87 LEU LEU A . n A 1 50 VAL 50 88 88 VAL VAL A . n A 1 51 LYS 51 89 89 LYS LYS A . n A 1 52 LYS 52 90 90 LYS LYS A . n A 1 53 ILE 53 91 91 ILE ILE A . n A 1 54 GLY 54 92 92 GLY GLY A . n A 1 55 LYS 55 93 93 LYS LYS A . n A 1 56 ALA 56 94 94 ALA ALA A . n A 1 57 VAL 57 95 95 VAL VAL A . n A 1 58 GLU 58 96 96 GLU GLU A . n A 1 59 ASP 59 97 97 ASP ASP A . n A 1 60 SER 60 98 98 SER SER A . n A 1 61 LYS 61 99 99 LYS LYS A . n A 1 62 PRO 62 100 100 PRO PRO A . n A 1 63 TYR 63 101 101 TYR TYR A . n A 1 64 TRP 64 102 102 TRP TRP A . n A 1 65 GLU 65 103 103 GLU GLU A . n A 1 66 ALA 66 104 104 ALA ALA A . n A 1 67 ARG 67 105 105 ARG ARG A . n A 1 68 ARG 68 106 106 ARG ARG A . n A 1 69 VAL 69 107 107 VAL VAL A . n A 1 70 ALA 70 108 108 ALA ALA A . n A 1 71 ARG 71 109 109 ARG ARG A . n A 1 72 GLN 72 110 110 GLN GLN A . n A 1 73 ALA 73 111 111 ALA ALA A . n A 1 74 GLN 74 112 112 GLN GLN A . n A 1 75 LEU 75 113 113 LEU LEU A . n A 1 76 GLU 76 114 114 GLU GLU A . n A 1 77 ALA 77 115 115 ALA ALA A . n A 1 78 GLN 78 116 116 GLN GLN A . n A 1 79 LYS 79 117 117 LYS LYS A . n A 1 80 ALA 80 118 118 ALA ALA A . n A 1 81 THR 81 119 119 THR THR A . n A 1 82 GLN 82 120 120 GLN GLN A . n A 1 83 ASP 83 121 121 ASP ASP A . n A 1 84 PHE 84 122 122 PHE PHE A . n A 1 85 GLN 85 123 123 GLN GLN A . n A 1 86 ARG 86 124 124 ARG ARG A . n A 1 87 ALA 87 125 125 ALA ALA A . n A 1 88 THR 88 126 126 THR THR A . n A 1 89 GLU 89 127 127 GLU GLU A . n A 1 90 VAL 90 128 128 VAL VAL A . n A 1 91 LEU 91 129 129 LEU LEU A . n A 1 92 ARG 92 130 130 ARG ARG A . n A 1 93 ALA 93 131 131 ALA ALA A . n A 1 94 ALA 94 132 132 ALA ALA A . n A 1 95 LYS 95 133 133 LYS LYS A . n A 1 96 GLU 96 134 134 GLU GLU A . n A 1 97 THR 97 135 135 THR THR A . n A 1 98 ILE 98 136 136 ILE ILE A . n A 1 99 SER 99 137 137 SER SER A . n A 1 100 LEU 100 138 138 LEU LEU A . n A 1 101 ALA 101 139 139 ALA ALA A . n A 1 102 GLU 102 140 140 GLU GLU A . n A 1 103 GLN 103 141 141 GLN GLN A . n A 1 104 ARG 104 142 142 ARG ARG A . n A 1 105 LEU 105 143 143 LEU LEU A . n A 1 106 LEU 106 144 ? ? ? A . n A 1 107 GLU 107 145 ? ? ? A . n A 1 108 ASP 108 146 ? ? ? A . n A 1 109 ASP 109 147 ? ? ? A . n A 1 110 LYS 110 148 ? ? ? A . n A 1 111 ARG 111 149 ? ? ? A . n A 1 112 GLN 112 150 ? ? ? A . n A 1 113 PHE 113 151 151 PHE PHE A . n A 1 114 ASP 114 152 152 ASP ASP A . n A 1 115 SER 115 153 153 SER SER A . n A 1 116 ALA 116 154 154 ALA ALA A . n A 1 117 TRP 117 155 155 TRP TRP A . n A 1 118 GLN 118 156 156 GLN GLN A . n A 1 119 GLU 119 157 157 GLU GLU A . n A 1 120 MSE 120 158 158 MSE MSE A . n A 1 121 LEU 121 159 159 LEU LEU A . n A 1 122 ASN 122 160 160 ASN ASN A . n A 1 123 HIS 123 161 161 HIS HIS A . n A 1 124 ALA 124 162 162 ALA ALA A . n A 1 125 THR 125 163 163 THR THR A . n A 1 126 GLN 126 164 164 GLN GLN A . n A 1 127 ARG 127 165 165 ARG ARG A . n A 1 128 VAL 128 166 166 VAL VAL A . n A 1 129 ALA 129 167 167 ALA ALA A . n A 1 130 GLU 130 168 168 GLU GLU A . n A 1 131 ALA 131 169 169 ALA ALA A . n A 1 132 GLU 132 170 170 GLU GLU A . n A 1 133 GLN 133 171 171 GLN GLN A . n A 1 134 THR 134 172 172 THR THR A . n A 1 135 LYS 135 173 173 LYS LYS A . n A 1 136 THR 136 174 174 THR THR A . n A 1 137 ARG 137 175 175 ARG ARG A . n A 1 138 SER 138 176 176 SER SER A . n A 1 139 GLU 139 177 177 GLU GLU A . n A 1 140 LEU 140 178 178 LEU LEU A . n A 1 141 VAL 141 179 179 VAL VAL A . n A 1 142 HIS 142 180 180 HIS HIS A . n A 1 143 LYS 143 181 181 LYS LYS A . n A 1 144 GLU 144 182 182 GLU GLU A . n A 1 145 THR 145 183 183 THR THR A . n A 1 146 ALA 146 184 184 ALA ALA A . n A 1 147 ALA 147 185 185 ALA ALA A . n A 1 148 ARG 148 186 186 ARG ARG A . n A 1 149 TYR 149 187 187 TYR TYR A . n A 1 150 ASN 150 188 188 ASN ASN A . n A 1 151 ALA 151 189 189 ALA ALA A . n A 1 152 ALA 152 190 190 ALA ALA A . n A 1 153 MSE 153 191 191 MSE MSE A . n A 1 154 GLY 154 192 192 GLY GLY A . n A 1 155 ARG 155 193 193 ARG ARG A . n A 1 156 MSE 156 194 194 MSE MSE A . n A 1 157 ARG 157 195 195 ARG ARG A . n A 1 158 GLN 158 196 196 GLN GLN A . n A 1 159 LEU 159 197 197 LEU LEU A . n A 1 160 GLU 160 198 198 GLU GLU A . n A 1 161 LYS 161 199 199 LYS LYS A . n A 1 162 LYS 162 200 200 LYS LYS A . n A 1 163 LEU 163 201 201 LEU LEU A . n A 1 164 LYS 164 202 202 LYS LYS A . n A 1 165 ARG 165 203 203 ARG ARG A . n A 1 166 ALA 166 204 204 ALA ALA A . n A 1 167 ILE 167 205 205 ILE ILE A . n A 1 168 ASN 168 206 206 ASN ASN A . n A 1 169 LYS 169 207 207 LYS LYS A . n A 1 170 SER 170 208 208 SER SER A . n A 1 171 LYS 171 209 209 LYS LYS A . n A 1 172 PRO 172 210 210 PRO PRO A . n A 1 173 TYR 173 211 211 TYR TYR A . n A 1 174 PHE 174 212 212 PHE PHE A . n A 1 175 GLU 175 213 213 GLU GLU A . n A 1 176 LEU 176 214 214 LEU LEU A . n A 1 177 LYS 177 215 215 LYS LYS A . n A 1 178 ALA 178 216 216 ALA ALA A . n A 1 179 LYS 179 217 217 LYS LYS A . n A 1 180 TYR 180 218 218 TYR TYR A . n A 1 181 TYR 181 219 219 TYR TYR A . n A 1 182 VAL 182 220 220 VAL VAL A . n A 1 183 GLN 183 221 221 GLN GLN A . n A 1 184 LEU 184 222 222 LEU LEU A . n A 1 185 GLU 185 223 223 GLU GLU A . n A 1 186 GLN 186 224 224 GLN GLN A . n A 1 187 LEU 187 225 225 LEU LEU A . n A 1 188 LYS 188 226 226 LYS LYS A . n A 1 189 LYS 189 227 227 LYS LYS A . n A 1 190 THR 190 228 228 THR THR A . n A 1 191 VAL 191 229 229 VAL VAL A . n A 1 192 ASP 192 230 230 ASP ASP A . n A 1 193 ASP 193 231 231 ASP ASP A . n A 1 194 LEU 194 232 232 LEU LEU A . n A 1 195 GLN 195 233 233 GLN GLN A . n A 1 196 ALA 196 234 234 ALA ALA A . n A 1 197 LYS 197 235 235 LYS LYS A . n A 1 198 LEU 198 236 236 LEU LEU A . n A 1 199 THR 199 237 237 THR THR A . n A 1 200 LEU 200 238 238 LEU LEU A . n A 1 201 ALA 201 239 239 ALA ALA A . n A 1 202 LYS 202 240 240 LYS LYS A . n A 1 203 GLY 203 241 241 GLY GLY A . n A 1 204 GLU 204 242 242 GLU GLU A . n A 1 205 TYR 205 243 243 TYR TYR A . n A 1 206 LYS 206 244 244 LYS LYS A . n A 1 207 MSE 207 245 245 MSE MSE A . n A 1 208 ALA 208 246 246 ALA ALA A . n A 1 209 LEU 209 247 247 LEU LEU A . n A 1 210 LYS 210 248 248 LYS LYS A . n A 1 211 ASN 211 249 249 ASN ASN A . n A 1 212 LEU 212 250 250 LEU LEU A . n A 1 213 GLU 213 251 251 GLU GLU A . n A 1 214 MSE 214 252 252 MSE MSE A . n A 1 215 ILE 215 253 253 ILE ILE A . n A 1 216 SER 216 254 254 SER SER A . n A 1 217 ASP 217 255 255 ASP ASP A . n A 1 218 GLU 218 256 256 GLU GLU A . n A 1 219 ILE 219 257 257 ILE ILE A . n A 1 220 HIS 220 258 258 HIS HIS A . n A 1 221 GLU 221 259 259 GLU GLU A . n A 1 222 ALA 222 260 260 ALA ALA A . n A 1 223 ALA 223 261 ? ? ? A . n A 1 224 ALA 224 262 ? ? ? A . n A 1 225 SER 225 263 ? ? ? A . n A 1 226 SER 226 264 ? ? ? A . n A 1 227 ALA 227 265 ? ? ? A . n A 1 228 MSE 228 266 ? ? ? A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id SIN _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 301 _pdbx_nonpoly_scheme.pdb_mon_id SIN _pdbx_nonpoly_scheme.auth_mon_id SIN _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # 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 120 A MSE 158 ? MET 'modified residue' 2 A MSE 153 A MSE 191 ? MET 'modified residue' 3 A MSE 156 A MSE 194 ? MET 'modified residue' 4 A MSE 207 A MSE 245 ? MET 'modified residue' 5 A MSE 214 A MSE 252 ? MET 'modified residue' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 2019-03-20 2 'Structure model' 1 1 2019-03-27 # _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 ? # 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' 'Data collection' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author # 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.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 2 'Structure model' '_citation_author.identifier_ORCID' 11 2 'Structure model' '_citation_author.name' # 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 ? ? ? 1.9_1692 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id LYS _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 90 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -62.65 _pdbx_validate_torsion.psi -72.84 # 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 SER 39 ? A SER 1 2 1 Y 1 A HIS 40 ? A HIS 2 3 1 Y 1 A LEU 144 ? A LEU 106 4 1 Y 1 A GLU 145 ? A GLU 107 5 1 Y 1 A ASP 146 ? A ASP 108 6 1 Y 1 A ASP 147 ? A ASP 109 7 1 Y 1 A LYS 148 ? A LYS 110 8 1 Y 1 A ARG 149 ? A ARG 111 9 1 Y 1 A GLN 150 ? A GLN 112 10 1 Y 1 A ALA 261 ? A ALA 223 11 1 Y 1 A ALA 262 ? A ALA 224 12 1 Y 1 A SER 263 ? A SER 225 13 1 Y 1 A SER 264 ? A SER 226 14 1 Y 1 A ALA 265 ? A ALA 227 15 1 Y 1 A MSE 266 ? A MSE 228 # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 17K15072 _pdbx_audit_support.ordinal 1 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'SUCCINIC ACID' _pdbx_entity_nonpoly.comp_id SIN # _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 ? #