data_2YYO # _entry.id 2YYO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.332 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YYO RCSB RCSB027300 WWPDB D_1000027300 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id hss001000898.2 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YYO _pdbx_database_status.recvd_initial_deposition_date 2007-04-30 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kishishita, S.' 1 ? 'Uchikubo-Kamo, T.' 2 ? 'Murayama, K.' 3 ? 'Terada, T.' 4 ? 'Chen, L.' 5 ? 'Fu, Z.Q.' 6 ? 'Chrzas, J.' 7 ? 'Shirouzu, M.' 8 ? 'Wang, B.C.' 9 ? 'Yokoyama, S.' 10 ? 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 11 ? # _citation.id primary _citation.title 'Crystal structure of human SPRY domain' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kishishita, S.' 1 ? primary 'Uchikubo-Kamo, T.' 2 ? primary 'Murayama, K.' 3 ? primary 'Terada, T.' 4 ? primary 'Chen, L.' 5 ? primary 'Fu, Z.Q.' 6 ? primary 'Chrzas, J.' 7 ? primary 'Shirouzu, M.' 8 ? primary 'Wang, B.C.' 9 ? primary 'Yokoyama, S.' 10 ? # _cell.entry_id 2YYO _cell.length_a 52.107 _cell.length_b 52.107 _cell.length_c 108.583 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2YYO _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # 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 'SPRY domain-containing protein 3' 18261.812 1 ? ? 'SPRY domain' ? 2 water nat water 18.015 91 ? ? ? ? # _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 ;GSSGSSGFKHILVDGDTLSYHGNSGEVGCYVASRPLTKDSNYFEVSIVDSGVRGTIAVGLVPQYYSLDHQPGWLPDSVAY HADDGKLYNGRAKGRQFGSKCNSGDRIGCGIEPVSFDVQTAQIFFTKNGKRVGSTI(MSE)P(MSE)SPDGLFPAVG (MSE)HSLGEEVRLHLNAELSGPSSG ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSGSSGFKHILVDGDTLSYHGNSGEVGCYVASRPLTKDSNYFEVSIVDSGVRGTIAVGLVPQYYSLDHQPGWLPDSVAY HADDGKLYNGRAKGRQFGSKCNSGDRIGCGIEPVSFDVQTAQIFFTKNGKRVGSTIMPMSPDGLFPAVGMHSLGEEVRLH LNAELSGPSSG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hss001000898.2 # 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 SER n 1 3 SER n 1 4 GLY n 1 5 SER n 1 6 SER n 1 7 GLY n 1 8 PHE n 1 9 LYS n 1 10 HIS n 1 11 ILE n 1 12 LEU n 1 13 VAL n 1 14 ASP n 1 15 GLY n 1 16 ASP n 1 17 THR n 1 18 LEU n 1 19 SER n 1 20 TYR n 1 21 HIS n 1 22 GLY n 1 23 ASN n 1 24 SER n 1 25 GLY n 1 26 GLU n 1 27 VAL n 1 28 GLY n 1 29 CYS n 1 30 TYR n 1 31 VAL n 1 32 ALA n 1 33 SER n 1 34 ARG n 1 35 PRO n 1 36 LEU n 1 37 THR n 1 38 LYS n 1 39 ASP n 1 40 SER n 1 41 ASN n 1 42 TYR n 1 43 PHE n 1 44 GLU n 1 45 VAL n 1 46 SER n 1 47 ILE n 1 48 VAL n 1 49 ASP n 1 50 SER n 1 51 GLY n 1 52 VAL n 1 53 ARG n 1 54 GLY n 1 55 THR n 1 56 ILE n 1 57 ALA n 1 58 VAL n 1 59 GLY n 1 60 LEU n 1 61 VAL n 1 62 PRO n 1 63 GLN n 1 64 TYR n 1 65 TYR n 1 66 SER n 1 67 LEU n 1 68 ASP n 1 69 HIS n 1 70 GLN n 1 71 PRO n 1 72 GLY n 1 73 TRP n 1 74 LEU n 1 75 PRO n 1 76 ASP n 1 77 SER n 1 78 VAL n 1 79 ALA n 1 80 TYR n 1 81 HIS n 1 82 ALA n 1 83 ASP n 1 84 ASP n 1 85 GLY n 1 86 LYS n 1 87 LEU n 1 88 TYR n 1 89 ASN n 1 90 GLY n 1 91 ARG n 1 92 ALA n 1 93 LYS n 1 94 GLY n 1 95 ARG n 1 96 GLN n 1 97 PHE n 1 98 GLY n 1 99 SER n 1 100 LYS n 1 101 CYS n 1 102 ASN n 1 103 SER n 1 104 GLY n 1 105 ASP n 1 106 ARG n 1 107 ILE n 1 108 GLY n 1 109 CYS n 1 110 GLY n 1 111 ILE n 1 112 GLU n 1 113 PRO n 1 114 VAL n 1 115 SER n 1 116 PHE n 1 117 ASP n 1 118 VAL n 1 119 GLN n 1 120 THR n 1 121 ALA n 1 122 GLN n 1 123 ILE n 1 124 PHE n 1 125 PHE n 1 126 THR n 1 127 LYS n 1 128 ASN n 1 129 GLY n 1 130 LYS n 1 131 ARG n 1 132 VAL n 1 133 GLY n 1 134 SER n 1 135 THR n 1 136 ILE n 1 137 MSE n 1 138 PRO n 1 139 MSE n 1 140 SER n 1 141 PRO n 1 142 ASP n 1 143 GLY n 1 144 LEU n 1 145 PHE n 1 146 PRO n 1 147 ALA n 1 148 VAL n 1 149 GLY n 1 150 MSE n 1 151 HIS n 1 152 SER n 1 153 LEU n 1 154 GLY n 1 155 GLU n 1 156 GLU n 1 157 VAL n 1 158 ARG n 1 159 LEU n 1 160 HIS n 1 161 LEU n 1 162 ASN n 1 163 ALA n 1 164 GLU n 1 165 LEU n 1 166 SER n 1 167 GLY n 1 168 PRO n 1 169 SER n 1 170 SER n 1 171 GLY 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 ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene SPRYD3 _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 'Cell-free protein synthesis' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _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 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 PK050905-07 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SPRY3_HUMAN _struct_ref.pdbx_db_accession Q8NCJ5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;FKHILVDGDTLSYHGNSGEVGCYVASRPLTKDSNYFEVSIVDSGVRGTIAVGLVPQYYSLDHQPGWLPDSVAYHADDGKL YNGRAKGRQFGSKCNSGDRIGCGIEPVSFDVQTAQIFFTKNGKRVGSTIMPMSPDGLFPAVGMHSLGEEVRLHLNAEL ; _struct_ref.pdbx_align_begin 46 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YYO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 165 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8NCJ5 _struct_ref_seq.db_align_beg 46 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 203 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 8 _struct_ref_seq.pdbx_auth_seq_align_end 165 # 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 2YYO GLY A 1 ? UNP Q8NCJ5 ? ? 'expression tag' 1 1 1 2YYO SER A 2 ? UNP Q8NCJ5 ? ? 'expression tag' 2 2 1 2YYO SER A 3 ? UNP Q8NCJ5 ? ? 'expression tag' 3 3 1 2YYO GLY A 4 ? UNP Q8NCJ5 ? ? 'expression tag' 4 4 1 2YYO SER A 5 ? UNP Q8NCJ5 ? ? 'expression tag' 5 5 1 2YYO SER A 6 ? UNP Q8NCJ5 ? ? 'expression tag' 6 6 1 2YYO GLY A 7 ? UNP Q8NCJ5 ? ? 'expression tag' 7 7 1 2YYO SER A 166 ? UNP Q8NCJ5 ? ? 'expression tag' 166 8 1 2YYO GLY A 167 ? UNP Q8NCJ5 ? ? 'expression tag' 167 9 1 2YYO PRO A 168 ? UNP Q8NCJ5 ? ? 'expression tag' 168 10 1 2YYO SER A 169 ? UNP Q8NCJ5 ? ? 'expression tag' 169 11 1 2YYO SER A 170 ? UNP Q8NCJ5 ? ? 'expression tag' 170 12 1 2YYO GLY A 171 ? UNP Q8NCJ5 ? ? 'expression tag' 171 13 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 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.entry_id 2YYO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 39.02 _exptl_crystal.description 'The file contains Friedel pairs.' _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details '0.1M Tris, 1.6M Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.pdbx_collection_date 2006-11-15 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si II' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9789 1.0 2 0.9793 1.0 3 0.971 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 22-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9789, 0.9793, 0.971' # _reflns.entry_id 2YYO _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.0 _reflns.number_obs 18943 _reflns.number_all ? _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.098 _reflns.pdbx_netI_over_sigmaI 78.6 _reflns.B_iso_Wilson_estimate 12.0 _reflns.pdbx_redundancy 24.5 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.11 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.348 _reflns_shell.meanI_over_sigI_obs 20.4 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2YYO _refine.ls_number_reflns_obs 18943 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 213101.66 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 26.05 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 98.1 _refine.ls_R_factor_obs 0.218 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.218 _refine.ls_R_factor_R_free 0.261 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 943 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 27.9 _refine.aniso_B[1][1] 3.24 _refine.aniso_B[2][2] 3.24 _refine.aniso_B[3][3] -6.48 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.339151 _refine.solvent_model_param_bsol 40.1519 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'The file contains Friedel pairs.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 2YYO _refine_analyze.Luzzati_coordinate_error_obs 0.24 _refine_analyze.Luzzati_sigma_a_obs 0.12 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.31 _refine_analyze.Luzzati_sigma_a_free 0.21 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1214 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 91 _refine_hist.number_atoms_total 1305 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 26.05 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 26.4 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.78 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.13 _refine_ls_shell.number_reflns_R_work 2982 _refine_ls_shell.R_factor_R_work 0.225 _refine_ls_shell.percent_reflns_obs 97.1 _refine_ls_shell.R_factor_R_free 0.314 _refine_ls_shell.R_factor_R_free_error 0.026 _refine_ls_shell.percent_reflns_R_free 4.6 _refine_ls_shell.number_reflns_R_free 144 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' # _struct.entry_id 2YYO _struct.title 'Crystal structure of human SPRY domain' _struct.pdbx_descriptor 'SPRY domain-containing protein 3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YYO _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.text ;SPRY domain, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id PRO _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 113 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ASP _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 117 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id PRO _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 113 _struct_conf.end_auth_comp_id ASP _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 117 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _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 ILE 136 C ? ? ? 1_555 A MSE 137 N ? ? A ILE 136 A MSE 137 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale2 covale both ? A MSE 137 C ? ? ? 1_555 A PRO 138 N ? ? A MSE 137 A PRO 138 1_555 ? ? ? ? ? ? ? 1.344 ? ? covale3 covale both ? A PRO 138 C ? ? ? 1_555 A MSE 139 N ? ? A PRO 138 A MSE 139 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale4 covale both ? A MSE 139 C ? ? ? 1_555 A SER 140 N ? ? A MSE 139 A SER 140 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale5 covale both ? A GLY 149 C ? ? ? 1_555 A MSE 150 N ? ? A GLY 149 A MSE 150 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale6 covale both ? A MSE 150 C ? ? ? 1_555 A HIS 151 N ? ? A MSE 150 A HIS 151 1_555 ? ? ? ? ? ? ? 1.328 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 7 ? # 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel B 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 A 1 GLY A 7 ? LYS A 9 ? GLY A 7 LYS A 9 A 2 GLY A 28 ? VAL A 31 ? GLY A 28 VAL A 31 A 3 PHE A 145 ? MSE A 150 ? PHE A 145 MSE A 150 A 4 ALA A 57 ? VAL A 61 ? ALA A 57 VAL A 61 A 5 VAL A 78 ? HIS A 81 ? VAL A 78 HIS A 81 A 6 LEU A 87 ? TYR A 88 ? LEU A 87 TYR A 88 B 1 ILE A 11 ? ASP A 14 ? ILE A 11 ASP A 14 B 2 THR A 17 ? TYR A 20 ? THR A 17 TYR A 20 B 3 GLU A 155 ? HIS A 160 ? GLU A 155 HIS A 160 B 4 TYR A 42 ? SER A 50 ? TYR A 42 SER A 50 B 5 ARG A 106 ? ILE A 111 ? ARG A 106 ILE A 111 B 6 ALA A 121 ? LYS A 127 ? ALA A 121 LYS A 127 B 7 LYS A 130 ? MSE A 137 ? LYS A 130 MSE A 137 # 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 A 1 2 N GLY A 7 ? N GLY A 7 O VAL A 31 ? O VAL A 31 A 2 3 N GLY A 28 ? N GLY A 28 O MSE A 150 ? O MSE A 150 A 3 4 O PHE A 145 ? O PHE A 145 N VAL A 61 ? N VAL A 61 A 4 5 N VAL A 58 ? N VAL A 58 O TYR A 80 ? O TYR A 80 A 5 6 N ALA A 79 ? N ALA A 79 O TYR A 88 ? O TYR A 88 B 1 2 N LEU A 12 ? N LEU A 12 O SER A 19 ? O SER A 19 B 2 3 N LEU A 18 ? N LEU A 18 O VAL A 157 ? O VAL A 157 B 3 4 O HIS A 160 ? O HIS A 160 N GLU A 44 ? N GLU A 44 B 4 5 N VAL A 45 ? N VAL A 45 O ILE A 107 ? O ILE A 107 B 5 6 N GLY A 110 ? N GLY A 110 O PHE A 124 ? O PHE A 124 B 6 7 N PHE A 125 ? N PHE A 125 O VAL A 132 ? O VAL A 132 # _database_PDB_matrix.entry_id 2YYO _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2YYO _atom_sites.fract_transf_matrix[1][1] 0.019191 _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] 0.019191 _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] 0.009210 _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 1 ? ? ? A . n A 1 2 SER 2 2 ? ? ? A . n A 1 3 SER 3 3 ? ? ? A . n A 1 4 GLY 4 4 ? ? ? A . n A 1 5 SER 5 5 ? ? ? A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 PHE 8 8 8 PHE PHE A . n A 1 9 LYS 9 9 9 LYS LYS A . n A 1 10 HIS 10 10 10 HIS HIS A . n A 1 11 ILE 11 11 11 ILE ILE A . n A 1 12 LEU 12 12 12 LEU LEU A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 ASP 16 16 16 ASP ASP A . n A 1 17 THR 17 17 17 THR THR A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 SER 19 19 19 SER SER A . n A 1 20 TYR 20 20 20 TYR TYR A . n A 1 21 HIS 21 21 21 HIS HIS A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 ASN 23 23 23 ASN ASN A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 GLY 25 25 25 GLY GLY A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 CYS 29 29 29 CYS CYS A . n A 1 30 TYR 30 30 30 TYR TYR A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 ALA 32 32 32 ALA ALA A . n A 1 33 SER 33 33 33 SER SER A . n A 1 34 ARG 34 34 34 ARG ARG A . n A 1 35 PRO 35 35 35 PRO PRO A . n A 1 36 LEU 36 36 36 LEU LEU A . n A 1 37 THR 37 37 37 THR THR A . n A 1 38 LYS 38 38 38 LYS LYS A . n A 1 39 ASP 39 39 39 ASP ASP A . n A 1 40 SER 40 40 40 SER SER A . n A 1 41 ASN 41 41 41 ASN ASN A . n A 1 42 TYR 42 42 42 TYR TYR A . n A 1 43 PHE 43 43 43 PHE PHE A . n A 1 44 GLU 44 44 44 GLU GLU A . n A 1 45 VAL 45 45 45 VAL VAL A . n A 1 46 SER 46 46 46 SER SER A . n A 1 47 ILE 47 47 47 ILE ILE A . n A 1 48 VAL 48 48 48 VAL VAL A . n A 1 49 ASP 49 49 49 ASP ASP A . n A 1 50 SER 50 50 50 SER SER A . n A 1 51 GLY 51 51 51 GLY GLY A . n A 1 52 VAL 52 52 52 VAL VAL A . n A 1 53 ARG 53 53 53 ARG ARG A . n A 1 54 GLY 54 54 54 GLY GLY A . n A 1 55 THR 55 55 55 THR THR A . n A 1 56 ILE 56 56 56 ILE ILE A . n A 1 57 ALA 57 57 57 ALA ALA A . n A 1 58 VAL 58 58 58 VAL VAL A . n A 1 59 GLY 59 59 59 GLY GLY A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 VAL 61 61 61 VAL VAL A . n A 1 62 PRO 62 62 62 PRO PRO A . n A 1 63 GLN 63 63 63 GLN GLN A . n A 1 64 TYR 64 64 64 TYR TYR A . n A 1 65 TYR 65 65 65 TYR TYR A . n A 1 66 SER 66 66 66 SER SER A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 ASP 68 68 68 ASP ASP A . n A 1 69 HIS 69 69 69 HIS HIS A . n A 1 70 GLN 70 70 70 GLN GLN A . n A 1 71 PRO 71 71 71 PRO PRO A . n A 1 72 GLY 72 72 72 GLY GLY A . n A 1 73 TRP 73 73 73 TRP TRP A . n A 1 74 LEU 74 74 74 LEU LEU A . n A 1 75 PRO 75 75 75 PRO PRO A . n A 1 76 ASP 76 76 76 ASP ASP A . n A 1 77 SER 77 77 77 SER SER A . n A 1 78 VAL 78 78 78 VAL VAL A . n A 1 79 ALA 79 79 79 ALA ALA A . n A 1 80 TYR 80 80 80 TYR TYR A . n A 1 81 HIS 81 81 81 HIS HIS A . n A 1 82 ALA 82 82 82 ALA ALA A . n A 1 83 ASP 83 83 83 ASP ASP A . n A 1 84 ASP 84 84 84 ASP ASP A . n A 1 85 GLY 85 85 85 GLY GLY A . n A 1 86 LYS 86 86 86 LYS LYS A . n A 1 87 LEU 87 87 87 LEU LEU A . n A 1 88 TYR 88 88 88 TYR TYR A . n A 1 89 ASN 89 89 89 ASN ASN A . n A 1 90 GLY 90 90 90 GLY GLY A . n A 1 91 ARG 91 91 91 ARG ARG A . n A 1 92 ALA 92 92 92 ALA ALA A . n A 1 93 LYS 93 93 93 LYS LYS A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 ARG 95 95 95 ARG ARG A . n A 1 96 GLN 96 96 96 GLN GLN A . n A 1 97 PHE 97 97 97 PHE PHE A . n A 1 98 GLY 98 98 98 GLY GLY A . n A 1 99 SER 99 99 99 SER SER A . n A 1 100 LYS 100 100 100 LYS LYS A . n A 1 101 CYS 101 101 101 CYS CYS A . n A 1 102 ASN 102 102 102 ASN ASN A . n A 1 103 SER 103 103 103 SER SER A . n A 1 104 GLY 104 104 104 GLY GLY A . n A 1 105 ASP 105 105 105 ASP ASP A . n A 1 106 ARG 106 106 106 ARG ARG A . n A 1 107 ILE 107 107 107 ILE ILE A . n A 1 108 GLY 108 108 108 GLY GLY A . n A 1 109 CYS 109 109 109 CYS CYS A . n A 1 110 GLY 110 110 110 GLY GLY A . n A 1 111 ILE 111 111 111 ILE ILE A . n A 1 112 GLU 112 112 112 GLU GLU A . n A 1 113 PRO 113 113 113 PRO PRO A . n A 1 114 VAL 114 114 114 VAL VAL A . n A 1 115 SER 115 115 115 SER SER A . n A 1 116 PHE 116 116 116 PHE PHE A . n A 1 117 ASP 117 117 117 ASP ASP A . n A 1 118 VAL 118 118 118 VAL VAL A . n A 1 119 GLN 119 119 119 GLN GLN A . n A 1 120 THR 120 120 120 THR THR A . n A 1 121 ALA 121 121 121 ALA ALA A . n A 1 122 GLN 122 122 122 GLN GLN A . n A 1 123 ILE 123 123 123 ILE ILE A . n A 1 124 PHE 124 124 124 PHE PHE A . n A 1 125 PHE 125 125 125 PHE PHE A . n A 1 126 THR 126 126 126 THR THR A . n A 1 127 LYS 127 127 127 LYS LYS A . n A 1 128 ASN 128 128 128 ASN ASN A . n A 1 129 GLY 129 129 129 GLY GLY A . n A 1 130 LYS 130 130 130 LYS LYS A . n A 1 131 ARG 131 131 131 ARG ARG A . n A 1 132 VAL 132 132 132 VAL VAL A . n A 1 133 GLY 133 133 133 GLY GLY A . n A 1 134 SER 134 134 134 SER SER A . n A 1 135 THR 135 135 135 THR THR A . n A 1 136 ILE 136 136 136 ILE ILE A . n A 1 137 MSE 137 137 137 MSE MSE A . n A 1 138 PRO 138 138 138 PRO PRO A . n A 1 139 MSE 139 139 139 MSE MSE A . n A 1 140 SER 140 140 140 SER SER A . n A 1 141 PRO 141 141 141 PRO PRO A . n A 1 142 ASP 142 142 142 ASP ASP A . n A 1 143 GLY 143 143 143 GLY GLY A . n A 1 144 LEU 144 144 144 LEU LEU A . n A 1 145 PHE 145 145 145 PHE PHE A . n A 1 146 PRO 146 146 146 PRO PRO A . n A 1 147 ALA 147 147 147 ALA ALA A . n A 1 148 VAL 148 148 148 VAL VAL A . n A 1 149 GLY 149 149 149 GLY GLY A . n A 1 150 MSE 150 150 150 MSE MSE A . n A 1 151 HIS 151 151 151 HIS HIS A . n A 1 152 SER 152 152 152 SER SER A . n A 1 153 LEU 153 153 153 LEU LEU A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 GLU 155 155 155 GLU GLU A . n A 1 156 GLU 156 156 156 GLU GLU A . n A 1 157 VAL 157 157 157 VAL VAL A . n A 1 158 ARG 158 158 158 ARG ARG A . n A 1 159 LEU 159 159 159 LEU LEU A . n A 1 160 HIS 160 160 160 HIS HIS A . n A 1 161 LEU 161 161 161 LEU LEU A . n A 1 162 ASN 162 162 162 ASN ASN A . n A 1 163 ALA 163 163 163 ALA ALA A . n A 1 164 GLU 164 164 164 GLU GLU A . n A 1 165 LEU 165 165 165 LEU LEU A . n A 1 166 SER 166 166 ? ? ? A . n A 1 167 GLY 167 167 ? ? ? A . n A 1 168 PRO 168 168 ? ? ? A . n A 1 169 SER 169 169 ? ? ? A . n A 1 170 SER 170 170 ? ? ? A . n A 1 171 GLY 171 171 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # 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 HOH 1 172 2 HOH TIP A . B 2 HOH 2 173 4 HOH TIP A . B 2 HOH 3 174 8 HOH TIP A . B 2 HOH 4 175 9 HOH TIP A . B 2 HOH 5 176 10 HOH TIP A . B 2 HOH 6 177 11 HOH TIP A . B 2 HOH 7 178 12 HOH TIP A . B 2 HOH 8 179 13 HOH TIP A . B 2 HOH 9 180 14 HOH TIP A . B 2 HOH 10 181 15 HOH TIP A . B 2 HOH 11 182 16 HOH TIP A . B 2 HOH 12 183 17 HOH TIP A . B 2 HOH 13 184 18 HOH TIP A . B 2 HOH 14 185 19 HOH TIP A . B 2 HOH 15 186 20 HOH TIP A . B 2 HOH 16 187 21 HOH TIP A . B 2 HOH 17 188 22 HOH TIP A . B 2 HOH 18 189 23 HOH TIP A . B 2 HOH 19 190 24 HOH TIP A . B 2 HOH 20 191 26 HOH TIP A . B 2 HOH 21 192 27 HOH TIP A . B 2 HOH 22 193 28 HOH TIP A . B 2 HOH 23 194 29 HOH TIP A . B 2 HOH 24 195 30 HOH TIP A . B 2 HOH 25 196 31 HOH TIP A . B 2 HOH 26 197 32 HOH TIP A . B 2 HOH 27 198 33 HOH TIP A . B 2 HOH 28 199 34 HOH TIP A . B 2 HOH 29 200 35 HOH TIP A . B 2 HOH 30 201 36 HOH TIP A . B 2 HOH 31 202 37 HOH TIP A . B 2 HOH 32 203 39 HOH TIP A . B 2 HOH 33 204 42 HOH TIP A . B 2 HOH 34 205 44 HOH TIP A . B 2 HOH 35 206 45 HOH TIP A . B 2 HOH 36 207 46 HOH TIP A . B 2 HOH 37 208 49 HOH TIP A . B 2 HOH 38 209 50 HOH TIP A . B 2 HOH 39 210 51 HOH TIP A . B 2 HOH 40 211 52 HOH TIP A . B 2 HOH 41 212 54 HOH TIP A . B 2 HOH 42 213 55 HOH TIP A . B 2 HOH 43 214 56 HOH TIP A . B 2 HOH 44 215 58 HOH TIP A . B 2 HOH 45 216 59 HOH TIP A . B 2 HOH 46 217 60 HOH TIP A . B 2 HOH 47 218 62 HOH TIP A . B 2 HOH 48 219 63 HOH TIP A . B 2 HOH 49 220 64 HOH TIP A . B 2 HOH 50 221 65 HOH TIP A . B 2 HOH 51 222 66 HOH TIP A . B 2 HOH 52 223 67 HOH TIP A . B 2 HOH 53 224 68 HOH TIP A . B 2 HOH 54 225 69 HOH TIP A . B 2 HOH 55 226 70 HOH TIP A . B 2 HOH 56 227 71 HOH TIP A . B 2 HOH 57 228 72 HOH TIP A . B 2 HOH 58 229 74 HOH TIP A . B 2 HOH 59 230 75 HOH TIP A . B 2 HOH 60 231 76 HOH TIP A . B 2 HOH 61 232 79 HOH TIP A . B 2 HOH 62 233 80 HOH TIP A . B 2 HOH 63 234 81 HOH TIP A . B 2 HOH 64 235 83 HOH TIP A . B 2 HOH 65 236 84 HOH TIP A . B 2 HOH 66 237 85 HOH TIP A . B 2 HOH 67 238 88 HOH TIP A . B 2 HOH 68 239 89 HOH TIP A . B 2 HOH 69 240 90 HOH TIP A . B 2 HOH 70 241 91 HOH TIP A . B 2 HOH 71 242 92 HOH TIP A . B 2 HOH 72 243 93 HOH TIP A . B 2 HOH 73 244 95 HOH TIP A . B 2 HOH 74 245 96 HOH TIP A . B 2 HOH 75 246 98 HOH TIP A . B 2 HOH 76 247 99 HOH TIP A . B 2 HOH 77 248 101 HOH TIP A . B 2 HOH 78 249 103 HOH TIP A . B 2 HOH 79 250 104 HOH TIP A . B 2 HOH 80 251 105 HOH TIP A . B 2 HOH 81 252 106 HOH TIP A . B 2 HOH 82 253 107 HOH TIP A . B 2 HOH 83 254 108 HOH TIP A . B 2 HOH 84 255 109 HOH TIP A . B 2 HOH 85 256 110 HOH TIP A . B 2 HOH 86 257 111 HOH TIP A . B 2 HOH 87 258 113 HOH TIP A . B 2 HOH 88 259 114 HOH TIP A . B 2 HOH 89 260 115 HOH TIP A . B 2 HOH 90 261 116 HOH TIP A . B 2 HOH 91 262 117 HOH TIP 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 137 A MSE 137 ? MET SELENOMETHIONINE 2 A MSE 139 A MSE 139 ? MET SELENOMETHIONINE 3 A MSE 150 A MSE 150 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B 2 1 A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z+1/4 0.0000000000 1.0000000000 0.0000000000 26.0535000000 -1.0000000000 0.0000000000 0.0000000000 26.0535000000 0.0000000000 0.0000000000 1.0000000000 27.1457500000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 250 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2008-05-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-09-09 # _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' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Structure summary' # 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 3 'Structure model' citation 2 3 'Structure model' struct 3 3 'Structure model' struct_conn 4 3 '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 3 'Structure model' '_citation.title' 2 3 'Structure model' '_struct.title' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 HKL-2000 'data scaling' . ? 3 SOLVE phasing . ? 4 # 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 HIS A 21 ? ? -152.96 68.32 2 1 SER A 24 ? ? 27.64 97.66 3 1 PHE A 97 ? ? -144.32 -73.43 4 1 PHE A 116 ? ? -64.40 16.74 5 1 VAL A 118 ? ? 40.70 173.50 6 1 THR A 120 ? ? 174.28 141.66 7 1 PRO A 141 ? ? -78.21 -164.28 8 1 ASP A 142 ? ? 57.78 0.70 9 1 HIS A 151 ? ? -151.76 1.69 10 1 HIS A 160 ? ? -119.88 79.11 # 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 1 ? A GLY 1 2 1 Y 1 A SER 2 ? A SER 2 3 1 Y 1 A SER 3 ? A SER 3 4 1 Y 1 A GLY 4 ? A GLY 4 5 1 Y 1 A SER 5 ? A SER 5 6 1 Y 1 A SER 166 ? A SER 166 7 1 Y 1 A GLY 167 ? A GLY 167 8 1 Y 1 A PRO 168 ? A PRO 168 9 1 Y 1 A SER 169 ? A SER 169 10 1 Y 1 A SER 170 ? A SER 170 11 1 Y 1 A GLY 171 ? A GLY 171 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #