data_3JZV # _entry.id 3JZV # _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 3JZV RCSB RCSB055368 WWPDB D_1000055368 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id NYSGXRC-9492b _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3JZV _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-09-24 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ramagopal, U.A.' 1 ? 'Toro, R.' 2 ? 'Burley, S.K.' 3 0000-0002-2487-9713 'Almo, S.C.' 4 ? 'New York SGX Research Center for Structural Genomics (NYSGXRC)' 5 ? # _citation.id primary _citation.title 'Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 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 'Ramagopal, U.A.' 1 ? primary 'Toro, R.' 2 ? primary 'Burley, S.K.' 3 0000-0002-2487-9713 primary 'Almo, S.C.' 4 ? # _cell.length_a 90.886 _cell.length_b 90.886 _cell.length_c 161.252 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3JZV _cell.pdbx_unique_axis ? _cell.Z_PDB 18 _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.space_group_name_H-M 'H 3 2' _symmetry.entry_id 3JZV _symmetry.Int_Tables_number 155 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 'uncharacterized protein Rru_A2000' 18595.045 1 ? ? ? ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 3 water nat water 18.015 12 ? ? ? ? # _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)SLSDSNDDRPFRPFQSQYRWPGVDLLAYKEEGSAPFRSVTRQVLFSGNGLTGELRYFEVGPGGHSTLERHQHAHG V(MSE)ILKGRGHA(MSE)VGRAVSAVAPYDLVTIPGWSWHQFRAPADEALGFLC(MSE)VNAERDKPQLPTEADLA (MSE)LRADDAVAAFLDGLAGEGHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MSLSDSNDDRPFRPFQSQYRWPGVDLLAYKEEGSAPFRSVTRQVLFSGNGLTGELRYFEVGPGGHSTLERHQHAHGVMIL KGRGHAMVGRAVSAVAPYDLVTIPGWSWHQFRAPADEALGFLCMVNAERDKPQLPTEADLAMLRADDAVAAFLDGLAGEG HHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier NYSGXRC-9492b # 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 SER n 1 5 ASP n 1 6 SER n 1 7 ASN n 1 8 ASP n 1 9 ASP n 1 10 ARG n 1 11 PRO n 1 12 PHE n 1 13 ARG n 1 14 PRO n 1 15 PHE n 1 16 GLN n 1 17 SER n 1 18 GLN n 1 19 TYR n 1 20 ARG n 1 21 TRP n 1 22 PRO n 1 23 GLY n 1 24 VAL n 1 25 ASP n 1 26 LEU n 1 27 LEU n 1 28 ALA n 1 29 TYR n 1 30 LYS n 1 31 GLU n 1 32 GLU n 1 33 GLY n 1 34 SER n 1 35 ALA n 1 36 PRO n 1 37 PHE n 1 38 ARG n 1 39 SER n 1 40 VAL n 1 41 THR n 1 42 ARG n 1 43 GLN n 1 44 VAL n 1 45 LEU n 1 46 PHE n 1 47 SER n 1 48 GLY n 1 49 ASN n 1 50 GLY n 1 51 LEU n 1 52 THR n 1 53 GLY n 1 54 GLU n 1 55 LEU n 1 56 ARG n 1 57 TYR n 1 58 PHE n 1 59 GLU n 1 60 VAL n 1 61 GLY n 1 62 PRO n 1 63 GLY n 1 64 GLY n 1 65 HIS n 1 66 SER n 1 67 THR n 1 68 LEU n 1 69 GLU n 1 70 ARG n 1 71 HIS n 1 72 GLN n 1 73 HIS n 1 74 ALA n 1 75 HIS n 1 76 GLY n 1 77 VAL n 1 78 MSE n 1 79 ILE n 1 80 LEU n 1 81 LYS n 1 82 GLY n 1 83 ARG n 1 84 GLY n 1 85 HIS n 1 86 ALA n 1 87 MSE n 1 88 VAL n 1 89 GLY n 1 90 ARG n 1 91 ALA n 1 92 VAL n 1 93 SER n 1 94 ALA n 1 95 VAL n 1 96 ALA n 1 97 PRO n 1 98 TYR n 1 99 ASP n 1 100 LEU n 1 101 VAL n 1 102 THR n 1 103 ILE n 1 104 PRO n 1 105 GLY n 1 106 TRP n 1 107 SER n 1 108 TRP n 1 109 HIS n 1 110 GLN n 1 111 PHE n 1 112 ARG n 1 113 ALA n 1 114 PRO n 1 115 ALA n 1 116 ASP n 1 117 GLU n 1 118 ALA n 1 119 LEU n 1 120 GLY n 1 121 PHE n 1 122 LEU n 1 123 CYS n 1 124 MSE n 1 125 VAL n 1 126 ASN n 1 127 ALA n 1 128 GLU n 1 129 ARG n 1 130 ASP n 1 131 LYS n 1 132 PRO n 1 133 GLN n 1 134 LEU n 1 135 PRO n 1 136 THR n 1 137 GLU n 1 138 ALA n 1 139 ASP n 1 140 LEU n 1 141 ALA n 1 142 MSE n 1 143 LEU n 1 144 ARG n 1 145 ALA n 1 146 ASP n 1 147 ASP n 1 148 ALA n 1 149 VAL n 1 150 ALA n 1 151 ALA n 1 152 PHE n 1 153 LEU n 1 154 ASP n 1 155 GLY n 1 156 LEU n 1 157 ALA n 1 158 GLY n 1 159 GLU n 1 160 GLY n 1 161 HIS n 1 162 HIS n 1 163 HIS n 1 164 HIS n 1 165 HIS n 1 166 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_A2000 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_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 BL21(DE3)' _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)' _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 plasmid _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description 'BC-pSGX4(BC)' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q2RSU5_RHORT _struct_ref.pdbx_db_accession Q2RSU5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SDSNDDRPFRPFQSQYRWPGVDLLAYKEEGSAPFRSVTRQVLFSGNGLTGELRYFEVGPGGHSTLERHQHAHGVMILKGR GHAMVGRAVSAVAPYDLVTIPGWSWHQFRAPADEALGFLCMVNAERDKPQLPTEADLAMLRADDAVAAFLDGLAG ; _struct_ref.pdbx_align_begin 2 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3JZV _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 158 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q2RSU5 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 156 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 156 # 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 3JZV MSE A 1 ? UNP Q2RSU5 ? ? 'expression tag' -1 1 1 3JZV SER A 2 ? UNP Q2RSU5 ? ? 'expression tag' 0 2 1 3JZV LEU A 3 ? UNP Q2RSU5 ? ? 'expression tag' 1 3 1 3JZV GLU A 159 ? UNP Q2RSU5 ? ? 'expression tag' 157 4 1 3JZV GLY A 160 ? UNP Q2RSU5 ? ? 'expression tag' 158 5 1 3JZV HIS A 161 ? UNP Q2RSU5 ? ? 'expression tag' 159 6 1 3JZV HIS A 162 ? UNP Q2RSU5 ? ? 'expression tag' 160 7 1 3JZV HIS A 163 ? UNP Q2RSU5 ? ? 'expression tag' 161 8 1 3JZV HIS A 164 ? UNP Q2RSU5 ? ? 'expression tag' 162 9 1 3JZV HIS A 165 ? UNP Q2RSU5 ? ? 'expression tag' 163 10 1 3JZV HIS A 166 ? UNP Q2RSU5 ? ? 'expression tag' 164 11 # 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 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 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.crystals_number 1 _exptl.entry_id 3JZV _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.45 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 64.31 _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.pH 7.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '15 % MPD, 0.1M Sodium Hepes pH 7.5, 0.8M Potassium Sodium Tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2009-08-02 ? 2 CCD 'ADSC QUANTUM 315' 2009-01-01 ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9793 1.0 2 0.979 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline 1 SYNCHROTRON 'APS BEAMLINE 24-ID-E' 0.9793 ? APS 24-ID-E 2 SYNCHROTRON 'NSLS BEAMLINE X29A' 0.979 ? NSLS X29A # _reflns.entry_id 3JZV _reflns.d_resolution_high 2.300 _reflns.d_resolution_low 25.000 _reflns.number_obs 11778 _reflns.pdbx_Rmerge_I_obs 0.106 _reflns.pdbx_netI_over_sigmaI 12.800 _reflns.pdbx_chi_squared 1.734 _reflns.pdbx_redundancy 7.000 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.30 2.34 ? ? ? 0.416 ? ? 0.914 7.30 ? 568 100.00 1 1 2.34 2.38 ? ? ? 0.330 ? ? 0.959 7.20 ? 581 100.00 2 1 2.38 2.43 ? ? ? 0.291 ? ? 0.886 7.20 ? 588 100.00 3 1 2.43 2.48 ? ? ? 0.285 ? ? 0.971 7.20 ? 577 100.00 4 1 2.48 2.53 ? ? ? 0.233 ? ? 1.039 7.20 ? 581 100.00 5 1 2.53 2.59 ? ? ? 0.203 ? ? 1.050 7.20 ? 584 100.00 6 1 2.59 2.65 ? ? ? 0.180 ? ? 1.148 7.20 ? 578 100.00 7 1 2.65 2.73 ? ? ? 0.168 ? ? 1.320 7.10 ? 582 100.00 8 1 2.73 2.81 ? ? ? 0.149 ? ? 1.481 7.10 ? 586 100.00 9 1 2.81 2.90 ? ? ? 0.134 ? ? 1.614 7.00 ? 587 100.00 10 1 2.90 3.00 ? ? ? 0.123 ? ? 1.807 7.00 ? 587 100.00 11 1 3.00 3.12 ? ? ? 0.107 ? ? 1.901 7.00 ? 582 100.00 12 1 3.12 3.26 ? ? ? 0.106 ? ? 2.058 7.00 ? 593 100.00 13 1 3.26 3.43 ? ? ? 0.108 ? ? 2.330 7.00 ? 588 100.00 14 1 3.43 3.65 ? ? ? 0.100 ? ? 2.364 6.90 ? 586 100.00 15 1 3.65 3.93 ? ? ? 0.109 ? ? 2.443 6.80 ? 589 99.80 16 1 3.93 4.32 ? ? ? 0.099 ? ? 2.519 6.90 ? 596 99.80 17 1 4.32 4.94 ? ? ? 0.096 ? ? 2.649 6.70 ? 601 99.80 18 1 4.94 6.21 ? ? ? 0.090 ? ? 2.646 6.50 ? 617 100.00 19 1 6.21 25.00 ? ? ? 0.097 ? ? 2.874 6.20 ? 627 98.00 20 1 # _refine.entry_id 3JZV _refine.ls_d_res_high 2.300 _refine.ls_d_res_low 23.580 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.850 _refine.ls_number_reflns_obs 11648 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.227 _refine.ls_R_factor_R_work 0.225 _refine.ls_wR_factor_R_work 0.248 _refine.ls_R_factor_R_free 0.278 _refine.ls_wR_factor_R_free 0.306 _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 560 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 60.110 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 4.190 _refine.aniso_B[2][2] 4.190 _refine.aniso_B[3][3] -6.290 _refine.aniso_B[1][2] 2.100 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.945 _refine.correlation_coeff_Fo_to_Fc_free 0.927 _refine.overall_SU_R_Cruickshank_DPI 0.222 _refine.overall_SU_R_free 0.210 _refine.pdbx_overall_ESU_R 0.222 _refine.pdbx_overall_ESU_R_Free 0.210 _refine.overall_SU_ML 0.181 _refine.overall_SU_B 7.613 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.751 _refine.B_iso_max 102.69 _refine.B_iso_min 39.55 _refine.occupancy_max 1.00 _refine.occupancy_min 0.30 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1138 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 12 _refine_hist.number_atoms_total 1151 _refine_hist.d_res_high 2.300 _refine_hist.d_res_low 23.580 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1176 0.014 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1599 1.492 1.943 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 148 6.466 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 56 32.646 22.321 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 170 14.691 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 11 17.039 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 167 0.097 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 933 0.007 0.021 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 736 0.906 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1167 1.705 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 440 2.157 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 431 3.534 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.300 _refine_ls_shell.d_res_low 2.359 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 799 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.316 _refine_ls_shell.R_factor_R_free 0.398 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 52 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 851 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3JZV _struct.title 'Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.' _struct.pdbx_descriptor 'uncharacterized protein Rru_A2000' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3JZV _struct_keywords.text ;structural genomics, cupin-2 fold, unknown function, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ; _struct_keywords.pdbx_keywords 'structural genomics, unknown function' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 # 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 136 ? ALA A 145 ? THR A 134 ALA A 143 1 ? 10 HELX_P HELX_P2 2 ASP A 146 ? ASP A 154 ? ASP A 144 ASP A 152 1 ? 9 # _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 VAL 77 C ? ? ? 1_555 A MSE 78 N ? ? A VAL 75 A MSE 76 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale2 covale both ? A MSE 78 C ? ? ? 1_555 A ILE 79 N ? ? A MSE 76 A ILE 77 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale3 covale both ? A ALA 86 C ? ? ? 1_555 A MSE 87 N ? ? A ALA 84 A MSE 85 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale4 covale both ? A MSE 87 C ? ? ? 1_555 A VAL 88 N ? ? A MSE 85 A VAL 86 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale5 covale both ? A CYS 123 C ? ? ? 1_555 A MSE 124 N ? ? A CYS 121 A MSE 122 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale6 covale both ? A MSE 124 C ? ? ? 1_555 A VAL 125 N ? ? A MSE 122 A VAL 123 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale7 covale both ? A ALA 141 C ? ? ? 1_555 A MSE 142 N ? ? A ALA 139 A MSE 140 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale8 covale both ? A MSE 142 C ? ? ? 1_555 A LEU 143 N ? ? A MSE 140 A LEU 141 1_555 ? ? ? ? ? ? ? 1.334 ? ? metalc1 metalc ? ? A GLU 69 OE1 ? ? ? 1_555 B MN . MN ? ? A GLU 67 A MN 200 1_555 ? ? ? ? ? ? ? 2.280 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id PRO _struct_mon_prot_cis.label_seq_id 97 _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 95 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 TYR _struct_mon_prot_cis.pdbx_label_seq_id_2 98 _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 TYR _struct_mon_prot_cis.pdbx_auth_seq_id_2 96 _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 -3.76 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 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 ? 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 # 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 LEU A 26 ? ALA A 28 ? LEU A 24 ALA A 26 A 2 ARG A 38 ? PHE A 46 ? ARG A 36 PHE A 44 A 3 GLY A 53 ? HIS A 65 ? GLY A 51 HIS A 63 A 4 LEU A 119 ? ASN A 126 ? LEU A 117 ASN A 124 A 5 HIS A 75 ? GLY A 82 ? HIS A 73 GLY A 80 A 6 LEU A 100 ? ILE A 103 ? LEU A 98 ILE A 101 B 1 ALA A 91 ? VAL A 95 ? ALA A 89 VAL A 93 B 2 GLY A 84 ? VAL A 88 ? GLY A 82 VAL A 86 B 3 HIS A 109 ? ARG A 112 ? HIS A 107 ARG A 110 # 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 LEU A 27 ? N LEU A 25 O ARG A 42 ? O ARG A 40 A 2 3 N SER A 39 ? N SER A 37 O GLY A 61 ? O GLY A 59 A 3 4 N VAL A 60 ? N VAL A 58 O LEU A 119 ? O LEU A 117 A 4 5 O GLY A 120 ? O GLY A 118 N LEU A 80 ? N LEU A 78 A 5 6 N VAL A 77 ? N VAL A 75 O VAL A 101 ? O VAL A 99 B 1 2 O SER A 93 ? O SER A 91 N ALA A 86 ? N ALA A 84 B 2 3 N HIS A 85 ? N HIS A 83 O ARG A 112 ? O ARG A 110 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MN _struct_site.pdbx_auth_seq_id 200 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE MN A 200' # 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 4 GLU A 69 ? GLU A 67 . ? 1_555 ? 2 AC1 4 HIS A 71 ? HIS A 69 . ? 1_555 ? 3 AC1 4 HIS A 75 ? HIS A 73 . ? 1_555 ? 4 AC1 4 HIS A 109 ? HIS A 107 . ? 1_555 ? # _atom_sites.entry_id 3JZV _atom_sites.fract_transf_matrix[1][1] 0.011003 _atom_sites.fract_transf_matrix[1][2] 0.006352 _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] 0.012705 _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] 0.006201 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MN 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 MSE 1 -1 ? ? ? A . n A 1 2 SER 2 0 ? ? ? A . n A 1 3 LEU 3 1 ? ? ? A . n A 1 4 SER 4 2 ? ? ? A . n A 1 5 ASP 5 3 ? ? ? A . n A 1 6 SER 6 4 ? ? ? A . n A 1 7 ASN 7 5 ? ? ? A . n A 1 8 ASP 8 6 ? ? ? A . n A 1 9 ASP 9 7 ? ? ? A . n A 1 10 ARG 10 8 8 ARG ARG A . n A 1 11 PRO 11 9 9 PRO PRO A . n A 1 12 PHE 12 10 10 PHE PHE A . n A 1 13 ARG 13 11 11 ARG ARG A . n A 1 14 PRO 14 12 12 PRO PRO A . n A 1 15 PHE 15 13 13 PHE PHE A . n A 1 16 GLN 16 14 14 GLN GLN A . n A 1 17 SER 17 15 15 SER SER A . n A 1 18 GLN 18 16 16 GLN GLN A . n A 1 19 TYR 19 17 17 TYR TYR A . n A 1 20 ARG 20 18 18 ARG ARG A . n A 1 21 TRP 21 19 19 TRP TRP A . n A 1 22 PRO 22 20 20 PRO PRO A . n A 1 23 GLY 23 21 21 GLY GLY A . n A 1 24 VAL 24 22 22 VAL VAL A . n A 1 25 ASP 25 23 23 ASP ASP A . n A 1 26 LEU 26 24 24 LEU LEU A . n A 1 27 LEU 27 25 25 LEU LEU A . n A 1 28 ALA 28 26 26 ALA ALA A . n A 1 29 TYR 29 27 27 TYR TYR A . n A 1 30 LYS 30 28 28 LYS LYS A . n A 1 31 GLU 31 29 29 GLU GLU A . n A 1 32 GLU 32 30 30 GLU GLU A . n A 1 33 GLY 33 31 ? ? ? A . n A 1 34 SER 34 32 32 SER SER A . n A 1 35 ALA 35 33 33 ALA ALA A . n A 1 36 PRO 36 34 34 PRO PRO A . n A 1 37 PHE 37 35 35 PHE PHE A . n A 1 38 ARG 38 36 36 ARG ARG A . n A 1 39 SER 39 37 37 SER SER A . n A 1 40 VAL 40 38 38 VAL VAL A . n A 1 41 THR 41 39 39 THR THR A . n A 1 42 ARG 42 40 40 ARG ARG A . n A 1 43 GLN 43 41 41 GLN GLN A . n A 1 44 VAL 44 42 42 VAL VAL A . n A 1 45 LEU 45 43 43 LEU LEU A . n A 1 46 PHE 46 44 44 PHE PHE A . n A 1 47 SER 47 45 45 SER SER A . n A 1 48 GLY 48 46 46 GLY GLY A . n A 1 49 ASN 49 47 47 ASN ASN A . n A 1 50 GLY 50 48 48 GLY GLY A . n A 1 51 LEU 51 49 49 LEU LEU A . n A 1 52 THR 52 50 50 THR THR A . n A 1 53 GLY 53 51 51 GLY GLY A . n A 1 54 GLU 54 52 52 GLU GLU A . n A 1 55 LEU 55 53 53 LEU LEU A . n A 1 56 ARG 56 54 54 ARG ARG A . n A 1 57 TYR 57 55 55 TYR TYR A . n A 1 58 PHE 58 56 56 PHE PHE A . n A 1 59 GLU 59 57 57 GLU GLU A . n A 1 60 VAL 60 58 58 VAL VAL A . n A 1 61 GLY 61 59 59 GLY GLY A . n A 1 62 PRO 62 60 60 PRO PRO A . n A 1 63 GLY 63 61 61 GLY GLY A . n A 1 64 GLY 64 62 62 GLY GLY A . n A 1 65 HIS 65 63 63 HIS HIS A . n A 1 66 SER 66 64 64 SER SER A . n A 1 67 THR 67 65 65 THR THR A . n A 1 68 LEU 68 66 66 LEU LEU A . n A 1 69 GLU 69 67 67 GLU GLU A . n A 1 70 ARG 70 68 68 ARG ARG A . n A 1 71 HIS 71 69 69 HIS HIS A . n A 1 72 GLN 72 70 70 GLN GLN A . n A 1 73 HIS 73 71 71 HIS HIS A . n A 1 74 ALA 74 72 72 ALA ALA A . n A 1 75 HIS 75 73 73 HIS HIS A . n A 1 76 GLY 76 74 74 GLY GLY A . n A 1 77 VAL 77 75 75 VAL VAL A . n A 1 78 MSE 78 76 76 MSE MSE A . n A 1 79 ILE 79 77 77 ILE ILE A . n A 1 80 LEU 80 78 78 LEU LEU A . n A 1 81 LYS 81 79 79 LYS LYS A . n A 1 82 GLY 82 80 80 GLY GLY A . n A 1 83 ARG 83 81 81 ARG ARG A . n A 1 84 GLY 84 82 82 GLY GLY A . n A 1 85 HIS 85 83 83 HIS HIS A . n A 1 86 ALA 86 84 84 ALA ALA A . n A 1 87 MSE 87 85 85 MSE MSE A . n A 1 88 VAL 88 86 86 VAL VAL A . n A 1 89 GLY 89 87 87 GLY GLY A . n A 1 90 ARG 90 88 88 ARG ARG A . n A 1 91 ALA 91 89 89 ALA ALA A . n A 1 92 VAL 92 90 90 VAL VAL A . n A 1 93 SER 93 91 91 SER SER A . n A 1 94 ALA 94 92 92 ALA ALA A . n A 1 95 VAL 95 93 93 VAL VAL A . n A 1 96 ALA 96 94 94 ALA ALA A . n A 1 97 PRO 97 95 95 PRO PRO A . n A 1 98 TYR 98 96 96 TYR TYR A . n A 1 99 ASP 99 97 97 ASP ASP A . n A 1 100 LEU 100 98 98 LEU LEU A . n A 1 101 VAL 101 99 99 VAL VAL A . n A 1 102 THR 102 100 100 THR THR A . n A 1 103 ILE 103 101 101 ILE ILE A . n A 1 104 PRO 104 102 102 PRO PRO A . n A 1 105 GLY 105 103 103 GLY GLY A . n A 1 106 TRP 106 104 104 TRP TRP A . n A 1 107 SER 107 105 105 SER SER A . n A 1 108 TRP 108 106 106 TRP TRP A . n A 1 109 HIS 109 107 107 HIS HIS A . n A 1 110 GLN 110 108 108 GLN GLN A . n A 1 111 PHE 111 109 109 PHE PHE A . n A 1 112 ARG 112 110 110 ARG ARG A . n A 1 113 ALA 113 111 111 ALA ALA A . n A 1 114 PRO 114 112 112 PRO PRO A . n A 1 115 ALA 115 113 113 ALA ALA A . n A 1 116 ASP 116 114 114 ASP ASP A . n A 1 117 GLU 117 115 115 GLU GLU A . n A 1 118 ALA 118 116 116 ALA ALA A . n A 1 119 LEU 119 117 117 LEU LEU A . n A 1 120 GLY 120 118 118 GLY GLY A . n A 1 121 PHE 121 119 119 PHE PHE A . n A 1 122 LEU 122 120 120 LEU LEU A . n A 1 123 CYS 123 121 121 CYS CYS A . n A 1 124 MSE 124 122 122 MSE MSE A . n A 1 125 VAL 125 123 123 VAL VAL A . n A 1 126 ASN 126 124 124 ASN ASN A . n A 1 127 ALA 127 125 125 ALA ALA A . n A 1 128 GLU 128 126 126 GLU GLU A . n A 1 129 ARG 129 127 127 ARG ARG A . n A 1 130 ASP 130 128 128 ASP ASP A . n A 1 131 LYS 131 129 129 LYS LYS A . n A 1 132 PRO 132 130 130 PRO PRO A . n A 1 133 GLN 133 131 131 GLN GLN A . n A 1 134 LEU 134 132 132 LEU LEU A . n A 1 135 PRO 135 133 133 PRO PRO A . n A 1 136 THR 136 134 134 THR THR A . n A 1 137 GLU 137 135 135 GLU GLU A . n A 1 138 ALA 138 136 136 ALA ALA A . n A 1 139 ASP 139 137 137 ASP ASP A . n A 1 140 LEU 140 138 138 LEU LEU A . n A 1 141 ALA 141 139 139 ALA ALA A . n A 1 142 MSE 142 140 140 MSE MSE A . n A 1 143 LEU 143 141 141 LEU LEU A . n A 1 144 ARG 144 142 142 ARG ARG A . n A 1 145 ALA 145 143 143 ALA ALA A . n A 1 146 ASP 146 144 144 ASP ASP A . n A 1 147 ASP 147 145 145 ASP ASP A . n A 1 148 ALA 148 146 146 ALA ALA A . n A 1 149 VAL 149 147 147 VAL VAL A . n A 1 150 ALA 150 148 148 ALA ALA A . n A 1 151 ALA 151 149 149 ALA ALA A . n A 1 152 PHE 152 150 150 PHE PHE A . n A 1 153 LEU 153 151 151 LEU LEU A . n A 1 154 ASP 154 152 152 ASP ASP A . n A 1 155 GLY 155 153 153 GLY GLY A . n A 1 156 LEU 156 154 154 LEU LEU A . n A 1 157 ALA 157 155 155 ALA ALA A . n A 1 158 GLY 158 156 156 GLY GLY A . n A 1 159 GLU 159 157 ? ? ? A . n A 1 160 GLY 160 158 ? ? ? A . n A 1 161 HIS 161 159 ? ? ? A . n A 1 162 HIS 162 160 ? ? ? A . n A 1 163 HIS 163 161 ? ? ? A . n A 1 164 HIS 164 162 ? ? ? A . n A 1 165 HIS 165 163 ? ? ? A . n A 1 166 HIS 166 164 ? ? ? A . 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 B 2 MN 1 200 200 MN MN A . C 3 HOH 1 165 1 HOH HOH A . C 3 HOH 2 166 2 HOH HOH A . C 3 HOH 3 167 4 HOH HOH A . C 3 HOH 4 168 8 HOH HOH A . C 3 HOH 5 169 10 HOH HOH A . C 3 HOH 6 170 11 HOH HOH A . C 3 HOH 7 171 15 HOH HOH A . C 3 HOH 8 172 19 HOH HOH A . C 3 HOH 9 173 20 HOH HOH A . C 3 HOH 10 174 21 HOH HOH A . C 3 HOH 11 175 22 HOH HOH A . C 3 HOH 12 176 23 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 78 A MSE 76 ? MET SELENOMETHIONINE 2 A MSE 87 A MSE 85 ? MET SELENOMETHIONINE 3 A MSE 124 A MSE 122 ? MET SELENOMETHIONINE 4 A MSE 142 A MSE 140 ? 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_and_software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA hexameric 6 # 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,C 2 1,3,4,2,5,6 A,B,C # 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)' 2530 ? 1 MORE -37 ? 1 'SSA (A^2)' 15120 ? 2 'ABSA (A^2)' 15960 ? 2 MORE -152 ? 2 'SSA (A^2)' 37000 ? # 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,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 5_555 x-y,-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 6 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 2009-10-13 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 4 'Structure model' 1 3 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' 'Source and taxonomy' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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' software 2 4 'Structure model' audit_author 3 4 'Structure model' citation_author 4 4 'Structure model' struct_conn 5 4 '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' '_software.classification' 2 3 'Structure model' '_software.contact_author' 3 3 'Structure model' '_software.contact_author_email' 4 3 'Structure model' '_software.date' 5 3 'Structure model' '_software.language' 6 3 'Structure model' '_software.location' 7 3 'Structure model' '_software.name' 8 3 'Structure model' '_software.type' 9 3 'Structure model' '_software.version' 10 4 'Structure model' '_audit_author.identifier_ORCID' 11 4 'Structure model' '_citation_author.identifier_ORCID' 12 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 13 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 6 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 7 PHENIX . ? ? ? ? phasing ? ? ? # 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 36 ? ? -161.82 116.35 2 1 TYR A 96 ? ? -114.27 63.28 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ARG 8 ? CG ? A ARG 10 CG 2 1 Y 1 A ARG 8 ? CD ? A ARG 10 CD 3 1 Y 1 A ARG 8 ? NE ? A ARG 10 NE 4 1 Y 1 A ARG 8 ? CZ ? A ARG 10 CZ 5 1 Y 1 A ARG 8 ? NH1 ? A ARG 10 NH1 6 1 Y 1 A ARG 8 ? NH2 ? A ARG 10 NH2 7 1 Y 1 A LYS 28 ? CG ? A LYS 30 CG 8 1 Y 1 A LYS 28 ? CD ? A LYS 30 CD 9 1 Y 1 A LYS 28 ? CE ? A LYS 30 CE 10 1 Y 1 A LYS 28 ? NZ ? A LYS 30 NZ 11 1 Y 1 A LYS 129 ? CD ? A LYS 131 CD 12 1 Y 1 A LYS 129 ? CE ? A LYS 131 CE 13 1 Y 1 A LYS 129 ? NZ ? A LYS 131 NZ # 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 -1 ? A MSE 1 2 1 Y 1 A SER 0 ? A SER 2 3 1 Y 1 A LEU 1 ? A LEU 3 4 1 Y 1 A SER 2 ? A SER 4 5 1 Y 1 A ASP 3 ? A ASP 5 6 1 Y 1 A SER 4 ? A SER 6 7 1 Y 1 A ASN 5 ? A ASN 7 8 1 Y 1 A ASP 6 ? A ASP 8 9 1 Y 1 A ASP 7 ? A ASP 9 10 1 Y 1 A GLY 31 ? A GLY 33 11 1 Y 1 A GLU 157 ? A GLU 159 12 1 Y 1 A GLY 158 ? A GLY 160 13 1 Y 1 A HIS 159 ? A HIS 161 14 1 Y 1 A HIS 160 ? A HIS 162 15 1 Y 1 A HIS 161 ? A HIS 163 16 1 Y 1 A HIS 162 ? A HIS 164 17 1 Y 1 A HIS 163 ? A HIS 165 18 1 Y 1 A HIS 164 ? A HIS 166 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 water HOH #