data_2CZT # _entry.id 2CZT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _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 2CZT pdb_00002czt 10.2210/pdb2czt/pdb RCSB RCSB024810 ? ? WWPDB D_1000024810 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2CZU _pdbx_database_related.details 'P212121 native form' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2CZT _pdbx_database_status.recvd_initial_deposition_date 2005-07-17 _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 'Kumasaka, T.' 1 'Irikura, D.' 2 'Ago, H.' 3 'Aritake, K.' 4 'Yamamoto, M.' 5 'Inoue, T.' 6 'Miyano, M.' 7 'Urade, Y.' 8 'Hayaishi, O.' 9 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 10 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structural basis of the catalytic mechanism operating in open-closed conformers of lipocalin type prostaglandin D synthase.' J.Biol.Chem. 284 22344 22352 2009 JBCHA3 US 0021-9258 0071 ? 19546224 10.1074/jbc.M109.018341 1 ;Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme ; 'J.Biochem.(Tokyo)' 133 29 32 2003 JOBIAO JA 0021-924X 0418 ? 12761195 10.1093/jb/mvg006 2 'Lack of tactile pain (allodynia) in lipocalin-type prostaglandin D synthase-deficient mice' Proc.Natl.Acad.Sci.USA 96 726 730 1999 PNASA6 US 0027-8424 0040 ? 9892701 10.1073/pnas.96.2.726 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kumasaka, T.' 1 ? primary 'Aritake, K.' 2 ? primary 'Ago, H.' 3 ? primary 'Irikura, D.' 4 ? primary 'Tsurumura, T.' 5 ? primary 'Yamamoto, M.' 6 ? primary 'Miyano, M.' 7 ? primary 'Urade, Y.' 8 ? primary 'Hayaishi, O.' 9 ? 1 'Irikura, D.' 10 ? 1 'Kumasaka, T.' 11 ? 1 'Yamamoto, M.' 12 ? 1 'Ago, H.' 13 ? 1 'Miyano, M.' 14 ? 1 'Kubata, K.B.' 15 ? 1 'Sakai, H.' 16 ? 1 'Hayaishi, O.' 17 ? 1 'Urade, Y.' 18 ? 2 'Eguchi, N.' 19 ? 2 'Minami, T.' 20 ? 2 'Shirafuji, N.' 21 ? 2 'Kanaoka, Y.' 22 ? 2 'Tanaka, T.' 23 ? 2 'Nagata, A.' 24 ? 2 'Yoshida, N.' 25 ? 2 'Urade, Y.' 26 ? 2 'Ito, S.' 27 ? 2 'Hayaishi, O.' 28 ? # _cell.entry_id 2CZT _cell.length_a 46.3 _cell.length_b 67.1 _cell.length_c 104.6 _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 2CZT _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _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 'Prostaglandin-H2 D-isomerase' 18617.859 1 5.3.99.2 C65A ? ? 2 water nat water 18.015 32 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Lipocalin-type prostaglandin-D synthase, Glutathione-independent PGD synthetase, Prostaglandin-H2 D-isomerase, PGD2 synthase, PTGDS, PGDS ; # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GSQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMAKTVVAPSTEGGLNLTSTFLRKNQCETKIMVLQPAGAP GHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGPGQDFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEEDIVFLPQ PDKCIQE ; _entity_poly.pdbx_seq_one_letter_code_can ;GSQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMAKTVVAPSTEGGLNLTSTFLRKNQCETKIMVLQPAGAP GHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGPGQDFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEEDIVFLPQ PDKCIQE ; _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 GLY n 1 2 SER n 1 3 GLN n 1 4 GLY n 1 5 HIS n 1 6 ASP n 1 7 THR n 1 8 VAL n 1 9 GLN n 1 10 PRO n 1 11 ASN n 1 12 PHE n 1 13 GLN n 1 14 GLN n 1 15 ASP n 1 16 LYS n 1 17 PHE n 1 18 LEU n 1 19 GLY n 1 20 ARG n 1 21 TRP n 1 22 TYR n 1 23 SER n 1 24 ALA n 1 25 GLY n 1 26 LEU n 1 27 ALA n 1 28 SER n 1 29 ASN n 1 30 SER n 1 31 SER n 1 32 TRP n 1 33 PHE n 1 34 ARG n 1 35 GLU n 1 36 LYS n 1 37 LYS n 1 38 ALA n 1 39 VAL n 1 40 LEU n 1 41 TYR n 1 42 MET n 1 43 ALA n 1 44 LYS n 1 45 THR n 1 46 VAL n 1 47 VAL n 1 48 ALA n 1 49 PRO n 1 50 SER n 1 51 THR n 1 52 GLU n 1 53 GLY n 1 54 GLY n 1 55 LEU n 1 56 ASN n 1 57 LEU n 1 58 THR n 1 59 SER n 1 60 THR n 1 61 PHE n 1 62 LEU n 1 63 ARG n 1 64 LYS n 1 65 ASN n 1 66 GLN n 1 67 CYS n 1 68 GLU n 1 69 THR n 1 70 LYS n 1 71 ILE n 1 72 MET n 1 73 VAL n 1 74 LEU n 1 75 GLN n 1 76 PRO n 1 77 ALA n 1 78 GLY n 1 79 ALA n 1 80 PRO n 1 81 GLY n 1 82 HIS n 1 83 TYR n 1 84 THR n 1 85 TYR n 1 86 SER n 1 87 SER n 1 88 PRO n 1 89 HIS n 1 90 SER n 1 91 GLY n 1 92 SER n 1 93 ILE n 1 94 HIS n 1 95 SER n 1 96 VAL n 1 97 SER n 1 98 VAL n 1 99 VAL n 1 100 GLU n 1 101 ALA n 1 102 ASN n 1 103 TYR n 1 104 ASP n 1 105 GLU n 1 106 TYR n 1 107 ALA n 1 108 LEU n 1 109 LEU n 1 110 PHE n 1 111 SER n 1 112 ARG n 1 113 GLY n 1 114 THR n 1 115 LYS n 1 116 GLY n 1 117 PRO n 1 118 GLY n 1 119 GLN n 1 120 ASP n 1 121 PHE n 1 122 ARG n 1 123 MET n 1 124 ALA n 1 125 THR n 1 126 LEU n 1 127 TYR n 1 128 SER n 1 129 ARG n 1 130 THR n 1 131 GLN n 1 132 THR n 1 133 LEU n 1 134 LYS n 1 135 ASP n 1 136 GLU n 1 137 LEU n 1 138 LYS n 1 139 GLU n 1 140 LYS n 1 141 PHE n 1 142 THR n 1 143 THR n 1 144 PHE n 1 145 SER n 1 146 LYS n 1 147 ALA n 1 148 GLN n 1 149 GLY n 1 150 LEU n 1 151 THR n 1 152 GLU n 1 153 GLU n 1 154 ASP n 1 155 ILE n 1 156 VAL n 1 157 PHE n 1 158 LEU n 1 159 PRO n 1 160 GLN n 1 161 PRO n 1 162 ASP n 1 163 LYS n 1 164 CYS n 1 165 ILE n 1 166 GLN n 1 167 GLU 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 'house mouse' _entity_src_gen.gene_src_genus Mus _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _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 Escherichia _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 PTGDS_MOUSE _struct_ref.pdbx_db_accession O09114 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 25 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2CZT _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 167 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O09114 _struct_ref_seq.db_align_beg 25 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 189 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 25 _struct_ref_seq.pdbx_auth_seq_align_end 189 # 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 2CZT GLY A 1 ? UNP O09114 ? ? 'cloning artifact' 23 1 1 2CZT SER A 2 ? UNP O09114 ? ? 'cloning artifact' 24 2 1 2CZT ALA A 43 ? UNP O09114 CYS 65 'engineered mutation' 65 3 # 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 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 2CZT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.2 _exptl_crystal.density_percent_sol 44 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 295.5 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details 'sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K' _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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2000-10-10 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.01 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL45XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL45XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.01 # _reflns.entry_id 2CZT _reflns.number_all ? _reflns.number_obs 11368 _reflns.percent_possible_obs ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high ? _reflns.d_resolution_low ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 10.0 _reflns_shell.percent_possible_all 77.2 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2CZT _refine.ls_number_reflns_obs 7821 _refine.ls_number_reflns_all 8773 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 77.06 _refine.ls_R_factor_obs 0.245 _refine.ls_R_factor_all 0.245 _refine.ls_R_factor_R_work 0.242 _refine.ls_R_factor_R_free 0.278 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 850 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.931 _refine.correlation_coeff_Fo_to_Fc_free 0.917 _refine.B_iso_mean 36.411 _refine.aniso_B[1][1] -1.64 _refine.aniso_B[2][2] 0.84 _refine.aniso_B[3][3] 0.80 _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 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.365 _refine.pdbx_overall_ESU_R_Free 0.251 _refine.overall_SU_ML 0.181 _refine.overall_SU_B 6.452 _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1223 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 32 _refine_hist.number_atoms_total 1255 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 10.00 # 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 r_bond_refined_d 0.012 0.021 ? 1252 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.385 1.953 ? 1690 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 3.838 3.000 ? 153 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.391 15.000 ? 228 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.092 0.200 ? 183 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 943 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.295 0.300 ? 523 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.152 0.500 ? 117 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.441 0.300 ? 37 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.643 0.500 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.845 1.500 ? 770 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.768 2.000 ? 1237 'X-RAY DIFFRACTION' ? r_scbond_it 4.428 3.000 ? 482 'X-RAY DIFFRACTION' ? r_scangle_it 6.461 4.500 ? 453 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.000 _refine_ls_shell.d_res_low 2.050 _refine_ls_shell.number_reflns_R_work 490 _refine_ls_shell.R_factor_R_work 0.266 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.314 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 48 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2CZT _struct.title 'lipocalin-type prostaglandin D synthase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2CZT _struct_keywords.pdbx_keywords ISOMERASE _struct_keywords.text 'LIPOCALIN, C2221 native, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, Isomerase' # 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_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 1 GLN A 13 ? LEU A 18 ? GLN A 35 LEU A 40 5 ? 6 HELX_P HELX_P2 2 TRP A 32 ? LYS A 37 ? TRP A 54 LYS A 59 1 ? 6 HELX_P HELX_P3 3 LYS A 134 ? GLN A 148 ? LYS A 156 GLN A 170 1 ? 15 HELX_P HELX_P4 4 THR A 151 ? GLU A 153 ? THR A 173 GLU A 175 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id disulf1 _struct_conn.conn_type_id disulf _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 67 _struct_conn.ptnr1_label_atom_id SG _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 164 _struct_conn.ptnr2_label_atom_id SG _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 89 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 186 _struct_conn.ptnr2_symmetry 1_555 _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 2.034 _struct_conn.pdbx_value_order ? _struct_conn.pdbx_role ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 10 _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 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 A 6 7 ? anti-parallel A 7 8 ? anti-parallel A 8 9 ? anti-parallel A 9 10 ? 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 ILE A 155 ? PHE A 157 ? ILE A 177 PHE A 179 A 2 GLY A 19 ? SER A 28 ? GLY A 41 SER A 50 A 3 ARG A 122 ? SER A 128 ? ARG A 144 SER A 150 A 4 TYR A 106 ? ARG A 112 ? TYR A 128 ARG A 134 A 5 HIS A 94 ? ASN A 102 ? HIS A 116 ASN A 124 A 6 HIS A 82 ? TYR A 85 ? HIS A 104 TYR A 107 A 7 CYS A 67 ? PRO A 76 ? CYS A 89 PRO A 98 A 8 LEU A 55 ? LEU A 62 ? LEU A 77 LEU A 84 A 9 LYS A 44 ? PRO A 49 ? LYS A 66 PRO A 71 A 10 GLY A 19 ? SER A 28 ? GLY A 41 SER A 50 # 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 O VAL A 156 ? O VAL A 178 N LEU A 26 ? N LEU A 48 A 2 3 N ALA A 27 ? N ALA A 49 O ALA A 124 ? O ALA A 146 A 3 4 O THR A 125 ? O THR A 147 N LEU A 109 ? N LEU A 131 A 4 5 O LEU A 108 ? O LEU A 130 N VAL A 99 ? N VAL A 121 A 5 6 O VAL A 96 ? O VAL A 118 N TYR A 83 ? N TYR A 105 A 6 7 O THR A 84 ? O THR A 106 N GLN A 75 ? N GLN A 97 A 7 8 O MET A 72 ? O MET A 94 N LEU A 57 ? N LEU A 79 A 8 9 O ASN A 56 ? O ASN A 78 N ALA A 48 ? N ALA A 70 A 9 10 O VAL A 47 ? O VAL A 69 N GLY A 19 ? N GLY A 41 # _database_PDB_matrix.entry_id 2CZT _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 2CZT _atom_sites.fract_transf_matrix[1][1] 0.021604 _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] 0.014896 _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] 0.009563 _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 # 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 23 ? ? ? A . n A 1 2 SER 2 24 ? ? ? A . n A 1 3 GLN 3 25 ? ? ? A . n A 1 4 GLY 4 26 ? ? ? A . n A 1 5 HIS 5 27 ? ? ? A . n A 1 6 ASP 6 28 ? ? ? A . n A 1 7 THR 7 29 ? ? ? A . n A 1 8 VAL 8 30 ? ? ? A . n A 1 9 GLN 9 31 ? ? ? A . n A 1 10 PRO 10 32 ? ? ? A . n A 1 11 ASN 11 33 ? ? ? A . n A 1 12 PHE 12 34 34 PHE PHE A . n A 1 13 GLN 13 35 35 GLN GLN A . n A 1 14 GLN 14 36 36 GLN GLN A . n A 1 15 ASP 15 37 37 ASP ASP A . n A 1 16 LYS 16 38 38 LYS LYS A . n A 1 17 PHE 17 39 39 PHE PHE A . n A 1 18 LEU 18 40 40 LEU LEU A . n A 1 19 GLY 19 41 41 GLY GLY A . n A 1 20 ARG 20 42 42 ARG ARG A . n A 1 21 TRP 21 43 43 TRP TRP A . n A 1 22 TYR 22 44 44 TYR TYR A . n A 1 23 SER 23 45 45 SER SER A . n A 1 24 ALA 24 46 46 ALA ALA A . n A 1 25 GLY 25 47 47 GLY GLY A . n A 1 26 LEU 26 48 48 LEU LEU A . n A 1 27 ALA 27 49 49 ALA ALA A . n A 1 28 SER 28 50 50 SER SER A . n A 1 29 ASN 29 51 51 ASN ASN A . n A 1 30 SER 30 52 52 SER SER A . n A 1 31 SER 31 53 53 SER SER A . n A 1 32 TRP 32 54 54 TRP TRP A . n A 1 33 PHE 33 55 55 PHE PHE A . n A 1 34 ARG 34 56 56 ARG ARG A . n A 1 35 GLU 35 57 57 GLU GLU A . n A 1 36 LYS 36 58 58 LYS LYS A . n A 1 37 LYS 37 59 59 LYS LYS A . n A 1 38 ALA 38 60 60 ALA ALA A . n A 1 39 VAL 39 61 61 VAL VAL A . n A 1 40 LEU 40 62 62 LEU LEU A . n A 1 41 TYR 41 63 63 TYR TYR A . n A 1 42 MET 42 64 64 MET MET A . n A 1 43 ALA 43 65 65 ALA ALA A . n A 1 44 LYS 44 66 66 LYS LYS A . n A 1 45 THR 45 67 67 THR THR A . n A 1 46 VAL 46 68 68 VAL VAL A . n A 1 47 VAL 47 69 69 VAL VAL A . n A 1 48 ALA 48 70 70 ALA ALA A . n A 1 49 PRO 49 71 71 PRO PRO A . n A 1 50 SER 50 72 72 SER SER A . n A 1 51 THR 51 73 73 THR THR A . n A 1 52 GLU 52 74 74 GLU GLU A . n A 1 53 GLY 53 75 75 GLY GLY A . n A 1 54 GLY 54 76 76 GLY GLY A . n A 1 55 LEU 55 77 77 LEU LEU A . n A 1 56 ASN 56 78 78 ASN ASN A . n A 1 57 LEU 57 79 79 LEU LEU A . n A 1 58 THR 58 80 80 THR THR A . n A 1 59 SER 59 81 81 SER SER A . n A 1 60 THR 60 82 82 THR THR A . n A 1 61 PHE 61 83 83 PHE PHE A . n A 1 62 LEU 62 84 84 LEU LEU A . n A 1 63 ARG 63 85 85 ARG ARG A . n A 1 64 LYS 64 86 86 LYS LYS A . n A 1 65 ASN 65 87 87 ASN ASN A . n A 1 66 GLN 66 88 ? ? ? A . n A 1 67 CYS 67 89 89 CYS CYS A . n A 1 68 GLU 68 90 90 GLU GLU A . n A 1 69 THR 69 91 91 THR THR A . n A 1 70 LYS 70 92 92 LYS LYS A . n A 1 71 ILE 71 93 93 ILE ILE A . n A 1 72 MET 72 94 94 MET MET A . n A 1 73 VAL 73 95 95 VAL VAL A . n A 1 74 LEU 74 96 96 LEU LEU A . n A 1 75 GLN 75 97 97 GLN GLN A . n A 1 76 PRO 76 98 98 PRO PRO A . n A 1 77 ALA 77 99 99 ALA ALA A . n A 1 78 GLY 78 100 100 GLY GLY A . n A 1 79 ALA 79 101 101 ALA ALA A . n A 1 80 PRO 80 102 102 PRO PRO A . n A 1 81 GLY 81 103 103 GLY GLY A . n A 1 82 HIS 82 104 104 HIS HIS A . n A 1 83 TYR 83 105 105 TYR TYR A . n A 1 84 THR 84 106 106 THR THR A . n A 1 85 TYR 85 107 107 TYR TYR A . n A 1 86 SER 86 108 108 SER SER A . n A 1 87 SER 87 109 109 SER SER A . n A 1 88 PRO 88 110 110 PRO PRO A . n A 1 89 HIS 89 111 111 HIS HIS A . n A 1 90 SER 90 112 112 SER SER A . n A 1 91 GLY 91 113 113 GLY GLY A . n A 1 92 SER 92 114 114 SER SER A . n A 1 93 ILE 93 115 115 ILE ILE A . n A 1 94 HIS 94 116 116 HIS HIS A . n A 1 95 SER 95 117 117 SER SER A . n A 1 96 VAL 96 118 118 VAL VAL A . n A 1 97 SER 97 119 119 SER SER A . n A 1 98 VAL 98 120 120 VAL VAL A . n A 1 99 VAL 99 121 121 VAL VAL A . n A 1 100 GLU 100 122 122 GLU GLU A . n A 1 101 ALA 101 123 123 ALA ALA A . n A 1 102 ASN 102 124 124 ASN ASN A . n A 1 103 TYR 103 125 125 TYR TYR A . n A 1 104 ASP 104 126 126 ASP ASP A . n A 1 105 GLU 105 127 127 GLU GLU A . n A 1 106 TYR 106 128 128 TYR TYR A . n A 1 107 ALA 107 129 129 ALA ALA A . n A 1 108 LEU 108 130 130 LEU LEU A . n A 1 109 LEU 109 131 131 LEU LEU A . n A 1 110 PHE 110 132 132 PHE PHE A . n A 1 111 SER 111 133 133 SER SER A . n A 1 112 ARG 112 134 134 ARG ARG A . n A 1 113 GLY 113 135 135 GLY GLY A . n A 1 114 THR 114 136 136 THR THR A . n A 1 115 LYS 115 137 137 LYS LYS A . n A 1 116 GLY 116 138 138 GLY GLY A . n A 1 117 PRO 117 139 139 PRO PRO A . n A 1 118 GLY 118 140 140 GLY GLY A . n A 1 119 GLN 119 141 141 GLN GLN A . n A 1 120 ASP 120 142 142 ASP ASP A . n A 1 121 PHE 121 143 143 PHE PHE A . n A 1 122 ARG 122 144 144 ARG ARG A . n A 1 123 MET 123 145 145 MET MET A . n A 1 124 ALA 124 146 146 ALA ALA A . n A 1 125 THR 125 147 147 THR THR A . n A 1 126 LEU 126 148 148 LEU LEU A . n A 1 127 TYR 127 149 149 TYR TYR A . n A 1 128 SER 128 150 150 SER SER A . n A 1 129 ARG 129 151 151 ARG ARG A . n A 1 130 THR 130 152 152 THR THR A . n A 1 131 GLN 131 153 153 GLN GLN A . n A 1 132 THR 132 154 154 THR THR A . n A 1 133 LEU 133 155 155 LEU LEU A . n A 1 134 LYS 134 156 156 LYS LYS A . n A 1 135 ASP 135 157 157 ASP ASP A . n A 1 136 GLU 136 158 158 GLU GLU A . n A 1 137 LEU 137 159 159 LEU LEU A . n A 1 138 LYS 138 160 160 LYS LYS A . n A 1 139 GLU 139 161 161 GLU GLU A . n A 1 140 LYS 140 162 162 LYS LYS A . n A 1 141 PHE 141 163 163 PHE PHE A . n A 1 142 THR 142 164 164 THR THR A . n A 1 143 THR 143 165 165 THR THR A . n A 1 144 PHE 144 166 166 PHE PHE A . n A 1 145 SER 145 167 167 SER SER A . n A 1 146 LYS 146 168 168 LYS LYS A . n A 1 147 ALA 147 169 169 ALA ALA A . n A 1 148 GLN 148 170 170 GLN GLN A . n A 1 149 GLY 149 171 171 GLY GLY A . n A 1 150 LEU 150 172 172 LEU LEU A . n A 1 151 THR 151 173 173 THR THR A . n A 1 152 GLU 152 174 174 GLU GLU A . n A 1 153 GLU 153 175 175 GLU GLU A . n A 1 154 ASP 154 176 176 ASP ASP A . n A 1 155 ILE 155 177 177 ILE ILE A . n A 1 156 VAL 156 178 178 VAL VAL A . n A 1 157 PHE 157 179 179 PHE PHE A . n A 1 158 LEU 158 180 180 LEU LEU A . n A 1 159 PRO 159 181 181 PRO PRO A . n A 1 160 GLN 160 182 182 GLN GLN A . n A 1 161 PRO 161 183 183 PRO PRO A . n A 1 162 ASP 162 184 184 ASP ASP A . n A 1 163 LYS 163 185 185 LYS LYS A . n A 1 164 CYS 164 186 186 CYS CYS A . n A 1 165 ILE 165 187 187 ILE ILE A . n A 1 166 GLN 166 188 188 GLN GLN A . n A 1 167 GLU 167 189 189 GLU GLU A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _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 1 190 1 HOH HOH A . B 2 HOH 2 191 2 HOH HOH A . B 2 HOH 3 192 3 HOH HOH A . B 2 HOH 4 193 4 HOH HOH A . B 2 HOH 5 194 5 HOH HOH A . B 2 HOH 6 195 6 HOH HOH A . B 2 HOH 7 196 7 HOH HOH A . B 2 HOH 8 197 8 HOH HOH A . B 2 HOH 9 198 9 HOH HOH A . B 2 HOH 10 199 10 HOH HOH A . B 2 HOH 11 200 1 HOH HOH A . B 2 HOH 12 201 2 HOH HOH A . B 2 HOH 13 202 3 HOH HOH A . B 2 HOH 14 203 4 HOH HOH A . B 2 HOH 15 204 5 HOH HOH A . B 2 HOH 16 205 6 HOH HOH A . B 2 HOH 17 206 7 HOH HOH A . B 2 HOH 18 207 8 HOH HOH A . B 2 HOH 19 208 9 HOH HOH A . B 2 HOH 20 209 10 HOH HOH A . B 2 HOH 21 210 11 HOH HOH A . B 2 HOH 22 211 12 HOH HOH A . B 2 HOH 23 212 13 HOH HOH A . B 2 HOH 24 213 14 HOH HOH A . B 2 HOH 25 214 15 HOH HOH A . B 2 HOH 26 215 16 HOH HOH A . B 2 HOH 27 216 17 HOH HOH A . B 2 HOH 28 217 18 HOH HOH A . B 2 HOH 29 218 19 HOH HOH A . B 2 HOH 30 219 20 HOH HOH A . B 2 HOH 31 220 21 HOH HOH A . B 2 HOH 32 221 22 HOH HOH A . # _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 2006-10-03 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2021-11-10 # _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' Advisory 3 3 'Structure model' 'Version format compliance' 4 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 4 'Structure model' database_2 2 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_ref_seq_dif.details' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 18.3690 _pdbx_refine_tls.origin_y 14.6300 _pdbx_refine_tls.origin_z 10.1870 _pdbx_refine_tls.T[1][1] 0.0940 _pdbx_refine_tls.T[2][2] 0.2099 _pdbx_refine_tls.T[3][3] 0.0478 _pdbx_refine_tls.T[1][2] -0.0279 _pdbx_refine_tls.T[1][3] 0.0052 _pdbx_refine_tls.T[2][3] 0.0963 _pdbx_refine_tls.L[1][1] 5.6119 _pdbx_refine_tls.L[2][2] 1.7883 _pdbx_refine_tls.L[3][3] 5.3268 _pdbx_refine_tls.L[1][2] 0.1364 _pdbx_refine_tls.L[1][3] -0.4168 _pdbx_refine_tls.L[2][3] 0.1244 _pdbx_refine_tls.S[1][1] 0.0455 _pdbx_refine_tls.S[1][2] -0.6594 _pdbx_refine_tls.S[1][3] -0.4957 _pdbx_refine_tls.S[2][1] 0.3140 _pdbx_refine_tls.S[2][2] -0.0103 _pdbx_refine_tls.S[2][3] 0.0883 _pdbx_refine_tls.S[3][1] 0.3460 _pdbx_refine_tls.S[3][2] -0.1142 _pdbx_refine_tls.S[3][3] -0.0352 _pdbx_refine_tls.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 34 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 12 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 189 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 167 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.0 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CCP4 phasing . ? 4 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 OH A TYR 125 ? ? 1_555 OH A TYR 125 ? ? 4_565 1.66 2 1 NZ A LYS 59 ? ? 1_555 ND2 A ASN 87 ? ? 3_655 1.92 3 1 OD2 A ASP 37 ? ? 1_555 NH2 A ARG 144 ? ? 8_555 1.93 4 1 CE A LYS 59 ? ? 1_555 ND2 A ASN 87 ? ? 3_655 2.18 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CB _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ASP _pdbx_validate_rmsd_angle.auth_seq_id_1 126 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CG _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ASP _pdbx_validate_rmsd_angle.auth_seq_id_2 126 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OD2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ASP _pdbx_validate_rmsd_angle.auth_seq_id_3 126 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 123.90 _pdbx_validate_rmsd_angle.angle_target_value 118.30 _pdbx_validate_rmsd_angle.angle_deviation 5.60 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # 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 ARG A 56 ? ? -65.72 0.65 2 1 GLU A 57 ? ? -130.76 -57.46 3 1 SER A 108 ? ? -74.27 -133.84 4 1 PRO A 110 ? ? -74.97 -96.19 5 1 SER A 112 ? ? -124.22 -157.08 6 1 GLU A 127 ? ? -133.94 -55.97 7 1 THR A 136 ? ? -170.65 125.35 8 1 PRO A 139 ? ? -39.88 126.48 9 1 ASP A 184 ? ? -86.63 39.03 10 1 LYS A 185 ? ? -158.18 -93.55 11 1 CYS A 186 ? ? -65.73 50.99 12 1 ILE A 187 ? ? -157.31 -1.04 13 1 GLN A 188 ? ? -120.18 -69.95 # 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 23 ? A GLY 1 2 1 Y 1 A SER 24 ? A SER 2 3 1 Y 1 A GLN 25 ? A GLN 3 4 1 Y 1 A GLY 26 ? A GLY 4 5 1 Y 1 A HIS 27 ? A HIS 5 6 1 Y 1 A ASP 28 ? A ASP 6 7 1 Y 1 A THR 29 ? A THR 7 8 1 Y 1 A VAL 30 ? A VAL 8 9 1 Y 1 A GLN 31 ? A GLN 9 10 1 Y 1 A PRO 32 ? A PRO 10 11 1 Y 1 A ASN 33 ? A ASN 11 12 1 Y 1 A GLN 88 ? A GLN 66 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #