data_3R03 # _entry.id 3R03 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.338 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3R03 RCSB RCSB064320 WWPDB D_1000064320 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id NYSGXRC-11180c _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3R03 _pdbx_database_status.recvd_initial_deposition_date 2011-03-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _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 'Zhang, Z.' 1 ? 'Burley, S.K.' 2 0000-0002-2487-9713 'Swaminathan, S.' 3 ? 'New York SGX Research Center for Structural Genomics (NYSGXRC)' 4 ? # _citation.id primary _citation.title 'The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum' _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 'Zhang, Z.' 1 ? primary 'Burley, S.K.' 2 0000-0002-2487-9713 primary 'Swaminathan, S.' 3 ? # _cell.entry_id 3R03 _cell.length_a 107.466 _cell.length_b 107.466 _cell.length_c 50.312 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3R03 _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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 'NUDIX hydrolase' 16082.025 2 ? ? 'sequence database residues 18-151' ? 2 non-polymer syn "ADENOSINE-5'-DIPHOSPHATE" 427.201 1 ? ? ? ? 3 water nat water 18.015 48 ? ? ? ? # _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 ;(MSE)SLGLPILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAF ASHSYDTFHLL(MSE)PLYACRSWRGRATAREGQTLAWVRAERLREYP(MSE)PPADLPLIPILQDWLEGHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MSLGLPILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHS YDTFHLLMPLYACRSWRGRATAREGQTLAWVRAERLREYPMPPADLPLIPILQDWLEGHHHHHH ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier NYSGXRC-11180c # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 SER n 1 3 LEU n 1 4 GLY n 1 5 LEU n 1 6 PRO n 1 7 ILE n 1 8 LEU n 1 9 LEU n 1 10 VAL n 1 11 THR n 1 12 ALA n 1 13 ALA n 1 14 ALA n 1 15 LEU n 1 16 ILE n 1 17 ASP n 1 18 PRO n 1 19 ASP n 1 20 GLY n 1 21 ARG n 1 22 VAL n 1 23 LEU n 1 24 LEU n 1 25 ALA n 1 26 GLN n 1 27 ARG n 1 28 PRO n 1 29 PRO n 1 30 GLY n 1 31 LYS n 1 32 SER n 1 33 LEU n 1 34 ALA n 1 35 GLY n 1 36 LEU n 1 37 TRP n 1 38 GLU n 1 39 PHE n 1 40 PRO n 1 41 GLY n 1 42 GLY n 1 43 LYS n 1 44 LEU n 1 45 GLU n 1 46 PRO n 1 47 GLY n 1 48 GLU n 1 49 THR n 1 50 PRO n 1 51 GLU n 1 52 ALA n 1 53 ALA n 1 54 LEU n 1 55 VAL n 1 56 ARG n 1 57 GLU n 1 58 LEU n 1 59 ALA n 1 60 GLU n 1 61 GLU n 1 62 LEU n 1 63 GLY n 1 64 VAL n 1 65 ASP n 1 66 THR n 1 67 ARG n 1 68 ALA n 1 69 SER n 1 70 CYS n 1 71 LEU n 1 72 ALA n 1 73 PRO n 1 74 LEU n 1 75 ALA n 1 76 PHE n 1 77 ALA n 1 78 SER n 1 79 HIS n 1 80 SER n 1 81 TYR n 1 82 ASP n 1 83 THR n 1 84 PHE n 1 85 HIS n 1 86 LEU n 1 87 LEU n 1 88 MSE n 1 89 PRO n 1 90 LEU n 1 91 TYR n 1 92 ALA n 1 93 CYS n 1 94 ARG n 1 95 SER n 1 96 TRP n 1 97 ARG n 1 98 GLY n 1 99 ARG n 1 100 ALA n 1 101 THR n 1 102 ALA n 1 103 ARG n 1 104 GLU n 1 105 GLY n 1 106 GLN n 1 107 THR n 1 108 LEU n 1 109 ALA n 1 110 TRP n 1 111 VAL n 1 112 ARG n 1 113 ALA n 1 114 GLU n 1 115 ARG n 1 116 LEU n 1 117 ARG n 1 118 GLU n 1 119 TYR n 1 120 PRO n 1 121 MSE n 1 122 PRO n 1 123 PRO n 1 124 ALA n 1 125 ASP n 1 126 LEU n 1 127 PRO n 1 128 LEU n 1 129 ILE n 1 130 PRO n 1 131 ILE n 1 132 LEU n 1 133 GLN n 1 134 ASP n 1 135 TRP n 1 136 LEU n 1 137 GLU n 1 138 GLY n 1 139 HIS n 1 140 HIS n 1 141 HIS n 1 142 HIS n 1 143 HIS n 1 144 HIS 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 ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Rru_A0393 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'strain ATCC 11170' _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 'Rhodospirillum rubrum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 269796 _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 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)-codon+RIL(p)' _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 'BC-pSGX3 (BC)' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q2RXE7_RHORT _struct_ref.pdbx_db_accession Q2RXE7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;LGLPILLVTAAALIDPDGRVLLAQRPPGKSLAGLWEFPGGKLEPGETPEAALVRELAEELGVDTRASCLAPLAFASHSYD TFHLLMPLYACRSWRGRATAREGQTLAWVRAERLREYPMPPADLPLIPILQDWL ; _struct_ref.pdbx_align_begin 18 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3R03 A 3 ? 136 ? Q2RXE7 18 ? 151 ? 18 151 2 1 3R03 B 3 ? 136 ? Q2RXE7 18 ? 151 ? 18 151 # 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 3R03 MSE A 1 ? UNP Q2RXE7 ? ? 'expression tag' 16 1 1 3R03 SER A 2 ? UNP Q2RXE7 ? ? 'expression tag' 17 2 1 3R03 GLU A 137 ? UNP Q2RXE7 ? ? 'expression tag' 152 3 1 3R03 GLY A 138 ? UNP Q2RXE7 ? ? 'expression tag' 153 4 1 3R03 HIS A 139 ? UNP Q2RXE7 ? ? 'expression tag' 154 5 1 3R03 HIS A 140 ? UNP Q2RXE7 ? ? 'expression tag' 155 6 1 3R03 HIS A 141 ? UNP Q2RXE7 ? ? 'expression tag' 156 7 1 3R03 HIS A 142 ? UNP Q2RXE7 ? ? 'expression tag' 157 8 1 3R03 HIS A 143 ? UNP Q2RXE7 ? ? 'expression tag' 158 9 1 3R03 HIS A 144 ? UNP Q2RXE7 ? ? 'expression tag' 159 10 2 3R03 MSE B 1 ? UNP Q2RXE7 ? ? 'expression tag' 16 11 2 3R03 SER B 2 ? UNP Q2RXE7 ? ? 'expression tag' 17 12 2 3R03 GLU B 137 ? UNP Q2RXE7 ? ? 'expression tag' 152 13 2 3R03 GLY B 138 ? UNP Q2RXE7 ? ? 'expression tag' 153 14 2 3R03 HIS B 139 ? UNP Q2RXE7 ? ? 'expression tag' 154 15 2 3R03 HIS B 140 ? UNP Q2RXE7 ? ? 'expression tag' 155 16 2 3R03 HIS B 141 ? UNP Q2RXE7 ? ? 'expression tag' 156 17 2 3R03 HIS B 142 ? UNP Q2RXE7 ? ? 'expression tag' 157 18 2 3R03 HIS B 143 ? UNP Q2RXE7 ? ? 'expression tag' 158 19 2 3R03 HIS B 144 ? UNP Q2RXE7 ? ? 'expression tag' 159 20 # 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 ADP non-polymer n "ADENOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O10 P2' 427.201 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 3R03 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.61 _exptl_crystal.density_percent_sol 52.83 _exptl_crystal.description ? _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 4.6 _exptl_crystal_grow.pdbx_details '0.1 M Sodium acetate trihydarate pH 4.6, 8% PEG 4000, 10 mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2011-01-01 _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 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3R03 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.49 _reflns.number_obs 11862 _reflns.number_all ? _reflns.percent_possible_obs 99.07 _reflns.pdbx_Rmerge_I_obs 0.110 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 27.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 22 _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 2.49 _reflns_shell.d_res_low 2.58 _reflns_shell.percent_possible_all 99.9 _reflns_shell.Rmerge_I_obs 0.41 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.7 _reflns_shell.pdbx_redundancy 21 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1178 _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 3R03 _refine.ls_number_reflns_obs 11862 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 5.05 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.534 _refine.ls_d_res_high 2.491 _refine.ls_percent_reflns_obs 99.07 _refine.ls_R_factor_obs 0.2368 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2312 _refine.ls_R_factor_R_free 0.2856 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.04 _refine.ls_number_reflns_R_free 1191 _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 ? _refine.aniso_B[1][1] 4.6248 _refine.aniso_B[2][2] 4.6248 _refine.aniso_B[3][3] -9.2496 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.314 _refine.solvent_model_param_bsol 40.270 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.43 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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 29.54 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_ESU_R ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2020 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 48 _refine_hist.number_atoms_total 2095 _refine_hist.d_res_high 2.491 _refine_hist.d_res_low 46.534 # 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 f_bond_d 0.006 ? ? 2110 'X-RAY DIFFRACTION' ? f_angle_d 0.969 ? ? 2893 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 15.562 ? ? 793 'X-RAY DIFFRACTION' ? f_chiral_restr 0.057 ? ? 322 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 371 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _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 . 2.4905 2.5902 1136 0.2707 96.00 0.3206 . . 129 . . . . 'X-RAY DIFFRACTION' . 2.5902 2.7081 1143 0.2579 98.00 0.3937 . . 133 . . . . 'X-RAY DIFFRACTION' . 2.7081 2.8509 1177 0.2532 99.00 0.3390 . . 132 . . . . 'X-RAY DIFFRACTION' . 2.8509 3.0295 1167 0.2504 99.00 0.2960 . . 131 . . . . 'X-RAY DIFFRACTION' . 3.0295 3.2633 1196 0.2479 100.00 0.3390 . . 127 . . . . 'X-RAY DIFFRACTION' . 3.2633 3.5916 1204 0.2347 100.00 0.3037 . . 136 . . . . 'X-RAY DIFFRACTION' . 3.5916 4.1111 1177 0.1981 99.00 0.2352 . . 129 . . . . 'X-RAY DIFFRACTION' . 4.1111 5.1784 1213 0.1711 100.00 0.2278 . . 130 . . . . 'X-RAY DIFFRACTION' . 5.1784 46.5422 1258 0.2393 100.00 0.2645 . . 144 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3R03 _struct.title 'The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum' _struct.pdbx_descriptor 'NUDIX hydrolase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3R03 _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'Structural Genomics, PSI2, HYDROLASE, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC' # 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details 'THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.' # 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 THR A 49 ? GLY A 63 ? THR A 64 GLY A 78 1 ? 15 HELX_P HELX_P2 2 ARG A 67 ? LEU A 71 ? ARG A 82 LEU A 86 5 ? 5 HELX_P HELX_P3 3 ARG A 112 ? TYR A 119 ? ARG A 127 TYR A 134 5 ? 8 HELX_P HELX_P4 4 PRO A 127 ? LEU A 136 ? PRO A 142 LEU A 151 1 ? 10 HELX_P HELX_P5 5 THR B 49 ? GLY B 63 ? THR B 64 GLY B 78 1 ? 15 HELX_P HELX_P6 6 ARG B 67 ? LEU B 71 ? ARG B 82 LEU B 86 5 ? 5 HELX_P HELX_P7 7 GLU B 114 ? TYR B 119 ? GLU B 129 TYR B 134 5 ? 6 HELX_P HELX_P8 8 PRO B 127 ? LEU B 136 ? PRO B 142 LEU B 151 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A LEU 87 C ? ? ? 1_555 A MSE 88 N ? ? A LEU 102 A MSE 103 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale2 covale both ? A MSE 88 C ? ? ? 1_555 A PRO 89 N ? ? A MSE 103 A PRO 104 1_555 ? ? ? ? ? ? ? 1.343 ? ? covale3 covale both ? A PRO 120 C ? ? ? 1_555 A MSE 121 N ? ? A PRO 135 A MSE 136 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale4 covale both ? A MSE 121 C ? ? ? 1_555 A PRO 122 N ? ? A MSE 136 A PRO 137 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale5 covale both ? B LEU 87 C ? ? ? 1_555 B MSE 88 N ? ? B LEU 102 B MSE 103 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale6 covale both ? B MSE 88 C ? ? ? 1_555 B PRO 89 N ? ? B MSE 103 B PRO 104 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale7 covale both ? B PRO 120 C ? ? ? 1_555 B MSE 121 N ? ? B PRO 135 B MSE 136 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale8 covale both ? B MSE 121 C ? ? ? 1_555 B PRO 122 N ? ? B MSE 136 B PRO 137 1_555 ? ? ? ? ? ? ? 1.340 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id PRO _struct_mon_prot_cis.label_seq_id 29 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id PRO _struct_mon_prot_cis.auth_seq_id 44 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 GLY _struct_mon_prot_cis.pdbx_label_seq_id_2 30 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 GLY _struct_mon_prot_cis.pdbx_auth_seq_id_2 45 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -4.45 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 3 ? C ? 3 ? D ? 3 ? E ? 3 ? # 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 ? parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel C 1 2 ? parallel C 2 3 ? parallel D 1 2 ? parallel D 2 3 ? anti-parallel E 1 2 ? anti-parallel E 2 3 ? 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 41 ? LYS A 43 ? GLY A 56 LYS A 58 A 2 ILE A 7 ? LEU A 15 ? ILE A 22 LEU A 30 A 3 HIS A 85 ? CYS A 93 ? HIS A 100 CYS A 108 A 4 ALA A 72 ? SER A 80 ? ALA A 87 SER A 95 B 1 TRP A 37 ? GLU A 38 ? TRP A 52 GLU A 53 B 2 VAL A 22 ? GLN A 26 ? VAL A 37 GLN A 41 B 3 THR A 107 ? VAL A 111 ? THR A 122 VAL A 126 C 1 ILE B 7 ? LEU B 9 ? ILE B 22 LEU B 24 C 2 HIS B 85 ? CYS B 93 ? HIS B 100 CYS B 108 C 3 ALA B 12 ? LEU B 15 ? ALA B 27 LEU B 30 D 1 ILE B 7 ? LEU B 9 ? ILE B 22 LEU B 24 D 2 HIS B 85 ? CYS B 93 ? HIS B 100 CYS B 108 D 3 ALA B 72 ? SER B 80 ? ALA B 87 SER B 95 E 1 TRP B 37 ? GLU B 38 ? TRP B 52 GLU B 53 E 2 ARG B 21 ? GLN B 26 ? ARG B 36 GLN B 41 E 3 THR B 107 ? ARG B 112 ? THR B 122 ARG B 127 # 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 GLY A 42 ? O GLY A 57 N THR A 11 ? N THR A 26 A 2 3 N ALA A 14 ? N ALA A 29 O TYR A 91 ? O TYR A 106 A 3 4 O LEU A 90 ? O LEU A 105 N ALA A 75 ? N ALA A 90 B 1 2 O GLU A 38 ? O GLU A 53 N ALA A 25 ? N ALA A 40 B 2 3 N LEU A 24 ? N LEU A 39 O ALA A 109 ? O ALA A 124 C 1 2 N LEU B 8 ? N LEU B 23 O HIS B 85 ? O HIS B 100 C 2 3 O TYR B 91 ? O TYR B 106 N ALA B 12 ? N ALA B 27 D 1 2 N LEU B 8 ? N LEU B 23 O HIS B 85 ? O HIS B 100 D 2 3 O LEU B 90 ? O LEU B 105 N ALA B 75 ? N ALA B 90 E 1 2 O GLU B 38 ? O GLU B 53 N ALA B 25 ? N ALA B 40 E 2 3 N VAL B 22 ? N VAL B 37 O VAL B 111 ? O VAL B 126 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id ADP _struct_site.pdbx_auth_seq_id 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE ADP A 1' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 ARG A 27 ? ARG A 42 . ? 1_555 ? 2 AC1 6 SER A 32 ? SER A 47 . ? 1_555 ? 3 AC1 6 GLU A 38 ? GLU A 53 . ? 1_555 ? 4 AC1 6 LYS A 43 ? LYS A 58 . ? 1_555 ? 5 AC1 6 MSE A 88 ? MSE A 103 . ? 1_555 ? 6 AC1 6 ASP A 125 ? ASP A 140 . ? 1_555 ? # _database_PDB_matrix.entry_id 3R03 _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 3R03 _atom_sites.fract_transf_matrix[1][1] 0.009305 _atom_sites.fract_transf_matrix[1][2] 0.005372 _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] 0.010745 _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] 0.019876 _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 P 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 MSE 1 16 ? ? ? A . n A 1 2 SER 2 17 ? ? ? A . n A 1 3 LEU 3 18 ? ? ? A . n A 1 4 GLY 4 19 ? ? ? A . n A 1 5 LEU 5 20 ? ? ? A . n A 1 6 PRO 6 21 21 PRO PRO A . n A 1 7 ILE 7 22 22 ILE ILE A . n A 1 8 LEU 8 23 23 LEU LEU A . n A 1 9 LEU 9 24 24 LEU LEU A . n A 1 10 VAL 10 25 25 VAL VAL A . n A 1 11 THR 11 26 26 THR THR A . n A 1 12 ALA 12 27 27 ALA ALA A . n A 1 13 ALA 13 28 28 ALA ALA A . n A 1 14 ALA 14 29 29 ALA ALA A . n A 1 15 LEU 15 30 30 LEU LEU A . n A 1 16 ILE 16 31 31 ILE ILE A . n A 1 17 ASP 17 32 32 ASP ASP A . n A 1 18 PRO 18 33 33 PRO PRO A . n A 1 19 ASP 19 34 34 ASP ASP A . n A 1 20 GLY 20 35 35 GLY GLY A . n A 1 21 ARG 21 36 36 ARG ARG A . n A 1 22 VAL 22 37 37 VAL VAL A . n A 1 23 LEU 23 38 38 LEU LEU A . n A 1 24 LEU 24 39 39 LEU LEU A . n A 1 25 ALA 25 40 40 ALA ALA A . n A 1 26 GLN 26 41 41 GLN GLN A . n A 1 27 ARG 27 42 42 ARG ARG A . n A 1 28 PRO 28 43 43 PRO PRO A . n A 1 29 PRO 29 44 44 PRO PRO A . n A 1 30 GLY 30 45 45 GLY GLY A . n A 1 31 LYS 31 46 46 LYS LYS A . n A 1 32 SER 32 47 47 SER SER A . n A 1 33 LEU 33 48 48 LEU LEU A . n A 1 34 ALA 34 49 49 ALA ALA A . n A 1 35 GLY 35 50 50 GLY GLY A . n A 1 36 LEU 36 51 51 LEU LEU A . n A 1 37 TRP 37 52 52 TRP TRP A . n A 1 38 GLU 38 53 53 GLU GLU A . n A 1 39 PHE 39 54 54 PHE PHE A . n A 1 40 PRO 40 55 55 PRO PRO A . n A 1 41 GLY 41 56 56 GLY GLY A . n A 1 42 GLY 42 57 57 GLY GLY A . n A 1 43 LYS 43 58 58 LYS LYS A . n A 1 44 LEU 44 59 59 LEU LEU A . n A 1 45 GLU 45 60 60 GLU GLU A . n A 1 46 PRO 46 61 61 PRO PRO A . n A 1 47 GLY 47 62 62 GLY GLY A . n A 1 48 GLU 48 63 63 GLU GLU A . n A 1 49 THR 49 64 64 THR THR A . n A 1 50 PRO 50 65 65 PRO PRO A . n A 1 51 GLU 51 66 66 GLU GLU A . n A 1 52 ALA 52 67 67 ALA ALA A . n A 1 53 ALA 53 68 68 ALA ALA A . n A 1 54 LEU 54 69 69 LEU LEU A . n A 1 55 VAL 55 70 70 VAL VAL A . n A 1 56 ARG 56 71 71 ARG ARG A . n A 1 57 GLU 57 72 72 GLU GLU A . n A 1 58 LEU 58 73 73 LEU LEU A . n A 1 59 ALA 59 74 74 ALA ALA A . n A 1 60 GLU 60 75 75 GLU GLU A . n A 1 61 GLU 61 76 76 GLU GLU A . n A 1 62 LEU 62 77 77 LEU LEU A . n A 1 63 GLY 63 78 78 GLY GLY A . n A 1 64 VAL 64 79 79 VAL VAL A . n A 1 65 ASP 65 80 80 ASP ASP A . n A 1 66 THR 66 81 81 THR THR A . n A 1 67 ARG 67 82 82 ARG ARG A . n A 1 68 ALA 68 83 83 ALA ALA A . n A 1 69 SER 69 84 84 SER SER A . n A 1 70 CYS 70 85 85 CYS CYS A . n A 1 71 LEU 71 86 86 LEU LEU A . n A 1 72 ALA 72 87 87 ALA ALA A . n A 1 73 PRO 73 88 88 PRO PRO A . n A 1 74 LEU 74 89 89 LEU LEU A . n A 1 75 ALA 75 90 90 ALA ALA A . n A 1 76 PHE 76 91 91 PHE PHE A . n A 1 77 ALA 77 92 92 ALA ALA A . n A 1 78 SER 78 93 93 SER SER A . n A 1 79 HIS 79 94 94 HIS HIS A . n A 1 80 SER 80 95 95 SER SER A . n A 1 81 TYR 81 96 96 TYR TYR A . n A 1 82 ASP 82 97 97 ASP ASP A . n A 1 83 THR 83 98 98 THR THR A . n A 1 84 PHE 84 99 99 PHE PHE A . n A 1 85 HIS 85 100 100 HIS HIS A . n A 1 86 LEU 86 101 101 LEU LEU A . n A 1 87 LEU 87 102 102 LEU LEU A . n A 1 88 MSE 88 103 103 MSE MSE A . n A 1 89 PRO 89 104 104 PRO PRO A . n A 1 90 LEU 90 105 105 LEU LEU A . n A 1 91 TYR 91 106 106 TYR TYR A . n A 1 92 ALA 92 107 107 ALA ALA A . n A 1 93 CYS 93 108 108 CYS CYS A . n A 1 94 ARG 94 109 109 ARG ARG A . n A 1 95 SER 95 110 110 SER SER A . n A 1 96 TRP 96 111 111 TRP TRP A . n A 1 97 ARG 97 112 112 ARG ARG A . n A 1 98 GLY 98 113 113 GLY GLY A . n A 1 99 ARG 99 114 114 ARG ARG A . n A 1 100 ALA 100 115 115 ALA ALA A . n A 1 101 THR 101 116 116 THR THR A . n A 1 102 ALA 102 117 117 ALA ALA A . n A 1 103 ARG 103 118 118 ARG ARG A . n A 1 104 GLU 104 119 119 GLU GLU A . n A 1 105 GLY 105 120 120 GLY GLY A . n A 1 106 GLN 106 121 121 GLN GLN A . n A 1 107 THR 107 122 122 THR THR A . n A 1 108 LEU 108 123 123 LEU LEU A . n A 1 109 ALA 109 124 124 ALA ALA A . n A 1 110 TRP 110 125 125 TRP TRP A . n A 1 111 VAL 111 126 126 VAL VAL A . n A 1 112 ARG 112 127 127 ARG ARG A . n A 1 113 ALA 113 128 128 ALA ALA A . n A 1 114 GLU 114 129 129 GLU GLU A . n A 1 115 ARG 115 130 130 ARG ARG A . n A 1 116 LEU 116 131 131 LEU LEU A . n A 1 117 ARG 117 132 132 ARG ARG A . n A 1 118 GLU 118 133 133 GLU GLU A . n A 1 119 TYR 119 134 134 TYR TYR A . n A 1 120 PRO 120 135 135 PRO PRO A . n A 1 121 MSE 121 136 136 MSE MSE A . n A 1 122 PRO 122 137 137 PRO PRO A . n A 1 123 PRO 123 138 138 PRO PRO A . n A 1 124 ALA 124 139 139 ALA ALA A . n A 1 125 ASP 125 140 140 ASP ASP A . n A 1 126 LEU 126 141 141 LEU LEU A . n A 1 127 PRO 127 142 142 PRO PRO A . n A 1 128 LEU 128 143 143 LEU LEU A . n A 1 129 ILE 129 144 144 ILE ILE A . n A 1 130 PRO 130 145 145 PRO PRO A . n A 1 131 ILE 131 146 146 ILE ILE A . n A 1 132 LEU 132 147 147 LEU LEU A . n A 1 133 GLN 133 148 148 GLN GLN A . n A 1 134 ASP 134 149 149 ASP ASP A . n A 1 135 TRP 135 150 150 TRP TRP A . n A 1 136 LEU 136 151 151 LEU LEU A . n A 1 137 GLU 137 152 ? ? ? A . n A 1 138 GLY 138 153 ? ? ? A . n A 1 139 HIS 139 154 ? ? ? A . n A 1 140 HIS 140 155 ? ? ? A . n A 1 141 HIS 141 156 ? ? ? A . n A 1 142 HIS 142 157 ? ? ? A . n A 1 143 HIS 143 158 ? ? ? A . n A 1 144 HIS 144 159 ? ? ? A . n B 1 1 MSE 1 16 ? ? ? B . n B 1 2 SER 2 17 ? ? ? B . n B 1 3 LEU 3 18 18 LEU LEU B . n B 1 4 GLY 4 19 19 GLY GLY B . n B 1 5 LEU 5 20 20 LEU LEU B . n B 1 6 PRO 6 21 21 PRO PRO B . n B 1 7 ILE 7 22 22 ILE ILE B . n B 1 8 LEU 8 23 23 LEU LEU B . n B 1 9 LEU 9 24 24 LEU LEU B . n B 1 10 VAL 10 25 25 VAL VAL B . n B 1 11 THR 11 26 26 THR THR B . n B 1 12 ALA 12 27 27 ALA ALA B . n B 1 13 ALA 13 28 28 ALA ALA B . n B 1 14 ALA 14 29 29 ALA ALA B . n B 1 15 LEU 15 30 30 LEU LEU B . n B 1 16 ILE 16 31 31 ILE ILE B . n B 1 17 ASP 17 32 32 ASP ASP B . n B 1 18 PRO 18 33 33 PRO PRO B . n B 1 19 ASP 19 34 34 ASP ASP B . n B 1 20 GLY 20 35 35 GLY GLY B . n B 1 21 ARG 21 36 36 ARG ARG B . n B 1 22 VAL 22 37 37 VAL VAL B . n B 1 23 LEU 23 38 38 LEU LEU B . n B 1 24 LEU 24 39 39 LEU LEU B . n B 1 25 ALA 25 40 40 ALA ALA B . n B 1 26 GLN 26 41 41 GLN GLN B . n B 1 27 ARG 27 42 42 ARG ARG B . n B 1 28 PRO 28 43 43 PRO PRO B . n B 1 29 PRO 29 44 44 PRO PRO B . n B 1 30 GLY 30 45 45 GLY GLY B . n B 1 31 LYS 31 46 ? ? ? B . n B 1 32 SER 32 47 ? ? ? B . n B 1 33 LEU 33 48 ? ? ? B . n B 1 34 ALA 34 49 ? ? ? B . n B 1 35 GLY 35 50 ? ? ? B . n B 1 36 LEU 36 51 51 LEU LEU B . n B 1 37 TRP 37 52 52 TRP TRP B . n B 1 38 GLU 38 53 53 GLU GLU B . n B 1 39 PHE 39 54 54 PHE PHE B . n B 1 40 PRO 40 55 55 PRO PRO B . n B 1 41 GLY 41 56 56 GLY GLY B . n B 1 42 GLY 42 57 57 GLY GLY B . n B 1 43 LYS 43 58 58 LYS LYS B . n B 1 44 LEU 44 59 59 LEU LEU B . n B 1 45 GLU 45 60 60 GLU GLU B . n B 1 46 PRO 46 61 61 PRO PRO B . n B 1 47 GLY 47 62 62 GLY GLY B . n B 1 48 GLU 48 63 63 GLU GLU B . n B 1 49 THR 49 64 64 THR THR B . n B 1 50 PRO 50 65 65 PRO PRO B . n B 1 51 GLU 51 66 66 GLU GLU B . n B 1 52 ALA 52 67 67 ALA ALA B . n B 1 53 ALA 53 68 68 ALA ALA B . n B 1 54 LEU 54 69 69 LEU LEU B . n B 1 55 VAL 55 70 70 VAL VAL B . n B 1 56 ARG 56 71 71 ARG ARG B . n B 1 57 GLU 57 72 72 GLU GLU B . n B 1 58 LEU 58 73 73 LEU LEU B . n B 1 59 ALA 59 74 74 ALA ALA B . n B 1 60 GLU 60 75 75 GLU GLU B . n B 1 61 GLU 61 76 76 GLU GLU B . n B 1 62 LEU 62 77 77 LEU LEU B . n B 1 63 GLY 63 78 78 GLY GLY B . n B 1 64 VAL 64 79 79 VAL VAL B . n B 1 65 ASP 65 80 80 ASP ASP B . n B 1 66 THR 66 81 81 THR THR B . n B 1 67 ARG 67 82 82 ARG ARG B . n B 1 68 ALA 68 83 83 ALA ALA B . n B 1 69 SER 69 84 84 SER SER B . n B 1 70 CYS 70 85 85 CYS CYS B . n B 1 71 LEU 71 86 86 LEU LEU B . n B 1 72 ALA 72 87 87 ALA ALA B . n B 1 73 PRO 73 88 88 PRO PRO B . n B 1 74 LEU 74 89 89 LEU LEU B . n B 1 75 ALA 75 90 90 ALA ALA B . n B 1 76 PHE 76 91 91 PHE PHE B . n B 1 77 ALA 77 92 92 ALA ALA B . n B 1 78 SER 78 93 93 SER SER B . n B 1 79 HIS 79 94 94 HIS HIS B . n B 1 80 SER 80 95 95 SER SER B . n B 1 81 TYR 81 96 96 TYR TYR B . n B 1 82 ASP 82 97 97 ASP ASP B . n B 1 83 THR 83 98 98 THR THR B . n B 1 84 PHE 84 99 99 PHE PHE B . n B 1 85 HIS 85 100 100 HIS HIS B . n B 1 86 LEU 86 101 101 LEU LEU B . n B 1 87 LEU 87 102 102 LEU LEU B . n B 1 88 MSE 88 103 103 MSE MSE B . n B 1 89 PRO 89 104 104 PRO PRO B . n B 1 90 LEU 90 105 105 LEU LEU B . n B 1 91 TYR 91 106 106 TYR TYR B . n B 1 92 ALA 92 107 107 ALA ALA B . n B 1 93 CYS 93 108 108 CYS CYS B . n B 1 94 ARG 94 109 109 ARG ARG B . n B 1 95 SER 95 110 110 SER SER B . n B 1 96 TRP 96 111 111 TRP TRP B . n B 1 97 ARG 97 112 112 ARG ARG B . n B 1 98 GLY 98 113 113 GLY GLY B . n B 1 99 ARG 99 114 114 ARG ARG B . n B 1 100 ALA 100 115 115 ALA ALA B . n B 1 101 THR 101 116 116 THR THR B . n B 1 102 ALA 102 117 117 ALA ALA B . n B 1 103 ARG 103 118 118 ARG ARG B . n B 1 104 GLU 104 119 119 GLU GLU B . n B 1 105 GLY 105 120 120 GLY GLY B . n B 1 106 GLN 106 121 121 GLN GLN B . n B 1 107 THR 107 122 122 THR THR B . n B 1 108 LEU 108 123 123 LEU LEU B . n B 1 109 ALA 109 124 124 ALA ALA B . n B 1 110 TRP 110 125 125 TRP TRP B . n B 1 111 VAL 111 126 126 VAL VAL B . n B 1 112 ARG 112 127 127 ARG ARG B . n B 1 113 ALA 113 128 128 ALA ALA B . n B 1 114 GLU 114 129 129 GLU GLU B . n B 1 115 ARG 115 130 130 ARG ARG B . n B 1 116 LEU 116 131 131 LEU LEU B . n B 1 117 ARG 117 132 132 ARG ARG B . n B 1 118 GLU 118 133 133 GLU GLU B . n B 1 119 TYR 119 134 134 TYR TYR B . n B 1 120 PRO 120 135 135 PRO PRO B . n B 1 121 MSE 121 136 136 MSE MSE B . n B 1 122 PRO 122 137 137 PRO PRO B . n B 1 123 PRO 123 138 138 PRO PRO B . n B 1 124 ALA 124 139 139 ALA ALA B . n B 1 125 ASP 125 140 140 ASP ASP B . n B 1 126 LEU 126 141 141 LEU LEU B . n B 1 127 PRO 127 142 142 PRO PRO B . n B 1 128 LEU 128 143 143 LEU LEU B . n B 1 129 ILE 129 144 144 ILE ILE B . n B 1 130 PRO 130 145 145 PRO PRO B . n B 1 131 ILE 131 146 146 ILE ILE B . n B 1 132 LEU 132 147 147 LEU LEU B . n B 1 133 GLN 133 148 148 GLN GLN B . n B 1 134 ASP 134 149 149 ASP ASP B . n B 1 135 TRP 135 150 150 TRP TRP B . n B 1 136 LEU 136 151 151 LEU LEU B . n B 1 137 GLU 137 152 ? ? ? B . n B 1 138 GLY 138 153 ? ? ? B . n B 1 139 HIS 139 154 ? ? ? B . n B 1 140 HIS 140 155 ? ? ? B . n B 1 141 HIS 141 156 ? ? ? B . n B 1 142 HIS 142 157 ? ? ? B . n B 1 143 HIS 143 158 ? ? ? B . n B 1 144 HIS 144 159 ? ? ? B . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'New York SGX Research Center for Structural Genomics' _pdbx_SG_project.initial_of_center NYSGXRC # 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 C 2 ADP 1 1 1 ADP ADP A . D 3 HOH 1 2 2 HOH HOH A . D 3 HOH 2 7 7 HOH HOH A . D 3 HOH 3 10 10 HOH HOH A . D 3 HOH 4 11 11 HOH HOH A . D 3 HOH 5 12 12 HOH HOH A . D 3 HOH 6 14 14 HOH HOH A . D 3 HOH 7 15 15 HOH HOH A . D 3 HOH 8 160 1 HOH HOH A . D 3 HOH 9 161 20 HOH HOH A . D 3 HOH 10 162 21 HOH HOH A . D 3 HOH 11 163 22 HOH HOH A . D 3 HOH 12 164 26 HOH HOH A . D 3 HOH 13 165 28 HOH HOH A . D 3 HOH 14 166 33 HOH HOH A . D 3 HOH 15 167 36 HOH HOH A . D 3 HOH 16 168 37 HOH HOH A . D 3 HOH 17 169 38 HOH HOH A . D 3 HOH 18 170 39 HOH HOH A . D 3 HOH 19 171 40 HOH HOH A . D 3 HOH 20 172 41 HOH HOH A . D 3 HOH 21 173 42 HOH HOH A . D 3 HOH 22 174 46 HOH HOH A . D 3 HOH 23 175 47 HOH HOH A . D 3 HOH 24 176 48 HOH HOH A . D 3 HOH 25 177 50 HOH HOH A . D 3 HOH 26 178 51 HOH HOH A . D 3 HOH 27 179 52 HOH HOH A . E 3 HOH 1 3 3 HOH HOH B . E 3 HOH 2 5 5 HOH HOH B . E 3 HOH 3 8 8 HOH HOH B . E 3 HOH 4 9 9 HOH HOH B . E 3 HOH 5 13 13 HOH HOH B . E 3 HOH 6 160 17 HOH HOH B . E 3 HOH 7 161 19 HOH HOH B . E 3 HOH 8 162 23 HOH HOH B . E 3 HOH 9 163 24 HOH HOH B . E 3 HOH 10 164 25 HOH HOH B . E 3 HOH 11 165 27 HOH HOH B . E 3 HOH 12 166 29 HOH HOH B . E 3 HOH 13 167 30 HOH HOH B . E 3 HOH 14 168 31 HOH HOH B . E 3 HOH 15 169 32 HOH HOH B . E 3 HOH 16 170 34 HOH HOH B . E 3 HOH 17 171 53 HOH HOH B . E 3 HOH 18 172 54 HOH HOH B . E 3 HOH 19 173 55 HOH HOH B . E 3 HOH 20 174 56 HOH HOH B . E 3 HOH 21 175 57 HOH HOH B . # 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 88 A MSE 103 ? MET SELENOMETHIONINE 2 A MSE 121 A MSE 136 ? MET SELENOMETHIONINE 3 B MSE 88 B MSE 103 ? MET SELENOMETHIONINE 4 B MSE 121 B MSE 136 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2150 ? 1 MORE -17 ? 1 'SSA (A^2)' 12840 ? # _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 2011-05-11 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2021-02-10 # _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' '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' audit_author 2 3 'Structure model' citation_author 3 3 'Structure model' struct_conn 4 3 'Structure model' struct_ref_seq_dif 5 3 'Structure model' struct_site # 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' '_audit_author.identifier_ORCID' 2 3 'Structure model' '_citation_author.identifier_ORCID' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq_dif.details' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 SOLVE phasing . ? 2 PHENIX refinement '(phenix.refine)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 ALA A 90 ? ? 174.09 -171.16 2 1 GLN A 121 ? ? -36.55 152.00 3 1 TYR B 96 ? ? -99.65 -157.83 4 1 ALA B 124 ? ? -171.65 124.18 # 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 MSE 16 ? A MSE 1 2 1 Y 1 A SER 17 ? A SER 2 3 1 Y 1 A LEU 18 ? A LEU 3 4 1 Y 1 A GLY 19 ? A GLY 4 5 1 Y 1 A LEU 20 ? A LEU 5 6 1 Y 1 A GLU 152 ? A GLU 137 7 1 Y 1 A GLY 153 ? A GLY 138 8 1 Y 1 A HIS 154 ? A HIS 139 9 1 Y 1 A HIS 155 ? A HIS 140 10 1 Y 1 A HIS 156 ? A HIS 141 11 1 Y 1 A HIS 157 ? A HIS 142 12 1 Y 1 A HIS 158 ? A HIS 143 13 1 Y 1 A HIS 159 ? A HIS 144 14 1 Y 1 B MSE 16 ? B MSE 1 15 1 Y 1 B SER 17 ? B SER 2 16 1 Y 1 B LYS 46 ? B LYS 31 17 1 Y 1 B SER 47 ? B SER 32 18 1 Y 1 B LEU 48 ? B LEU 33 19 1 Y 1 B ALA 49 ? B ALA 34 20 1 Y 1 B GLY 50 ? B GLY 35 21 1 Y 1 B GLU 152 ? B GLU 137 22 1 Y 1 B GLY 153 ? B GLY 138 23 1 Y 1 B HIS 154 ? B HIS 139 24 1 Y 1 B HIS 155 ? B HIS 140 25 1 Y 1 B HIS 156 ? B HIS 141 26 1 Y 1 B HIS 157 ? B HIS 142 27 1 Y 1 B HIS 158 ? B HIS 143 28 1 Y 1 B HIS 159 ? B HIS 144 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "ADENOSINE-5'-DIPHOSPHATE" ADP 3 water HOH #