data_3DUE # _entry.id 3DUE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _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 3DUE pdb_00003due 10.2210/pdb3due/pdb RCSB RCSB048500 ? ? WWPDB D_1000048500 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 390185 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3DUE _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-07-17 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function. ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 66 _citation.page_first 1265 _citation.page_last 1273 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20944221 _citation.pdbx_database_id_DOI 10.1107/S1744309109046788 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Das, D.' 1 ? primary 'Finn, R.D.' 2 ? primary 'Carlton, D.' 3 ? primary 'Miller, M.D.' 4 ? primary 'Abdubek, P.' 5 ? primary 'Astakhova, T.' 6 ? primary 'Axelrod, H.L.' 7 ? primary 'Bakolitsa, C.' 8 ? primary 'Chen, C.' 9 ? primary 'Chiu, H.J.' 10 ? primary 'Chiu, M.' 11 ? primary 'Clayton, T.' 12 ? primary 'Deller, M.C.' 13 ? primary 'Duan, L.' 14 ? primary 'Ellrott, K.' 15 ? primary 'Ernst, D.' 16 ? primary 'Farr, C.L.' 17 ? primary 'Feuerhelm, J.' 18 ? primary 'Grant, J.C.' 19 ? primary 'Grzechnik, A.' 20 ? primary 'Han, G.W.' 21 ? primary 'Jaroszewski, L.' 22 ? primary 'Jin, K.K.' 23 ? primary 'Klock, H.E.' 24 ? primary 'Knuth, M.W.' 25 ? primary 'Kozbial, P.' 26 ? primary 'Krishna, S.S.' 27 ? primary 'Kumar, A.' 28 ? primary 'Marciano, D.' 29 ? primary 'McMullan, D.' 30 ? primary 'Morse, A.T.' 31 ? primary 'Nigoghossian, E.' 32 ? primary 'Nopakun, A.' 33 ? primary 'Okach, L.' 34 ? primary 'Puckett, C.' 35 ? primary 'Reyes, R.' 36 ? primary 'Rife, C.L.' 37 ? primary 'Sefcovic, N.' 38 ? primary 'Tien, H.J.' 39 ? primary 'Trame, C.B.' 40 ? primary 'van den Bedem, H.' 41 ? primary 'Weekes, D.' 42 ? primary 'Wooten, T.' 43 ? primary 'Xu, Q.' 44 ? primary 'Hodgson, K.O.' 45 ? primary 'Wooley, J.' 46 ? primary 'Elsliger, M.A.' 47 ? primary 'Deacon, A.M.' 48 ? primary 'Godzik, A.' 49 ? primary 'Lesley, S.A.' 50 ? primary 'Wilson, I.A.' 51 ? # _cell.entry_id 3DUE _cell.length_a 31.601 _cell.length_b 50.874 _cell.length_c 79.507 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3DUE _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 'Putative periplasmic protein' 14889.206 1 ? ? ? ? 2 non-polymer syn 'CACODYLATE ION' 136.989 1 ? ? ? ? 3 water nat water 18.015 133 ? ? ? ? # _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 ;GADDDKPIQVNQLPQTAQTFIKTHFPDNKVA(MSE)AK(MSE)ETDWFDKSYDVIFTNGDKLEFDKKGIWTEVNCKYSAV PVAVVPDAIKKYVATNYPDAK(MSE)LKIERDKHDYEVKLSNGWEIKFD(MSE)QFNVIDIDN ; _entity_poly.pdbx_seq_one_letter_code_can ;GADDDKPIQVNQLPQTAQTFIKTHFPDNKVAMAKMETDWFDKSYDVIFTNGDKLEFDKKGIWTEVNCKYSAVPVAVVPDA IKKYVATNYPDAKMLKIERDKHDYEVKLSNGWEIKFDMQFNVIDIDN ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 390185 # 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 ALA n 1 3 ASP n 1 4 ASP n 1 5 ASP n 1 6 LYS n 1 7 PRO n 1 8 ILE n 1 9 GLN n 1 10 VAL n 1 11 ASN n 1 12 GLN n 1 13 LEU n 1 14 PRO n 1 15 GLN n 1 16 THR n 1 17 ALA n 1 18 GLN n 1 19 THR n 1 20 PHE n 1 21 ILE n 1 22 LYS n 1 23 THR n 1 24 HIS n 1 25 PHE n 1 26 PRO n 1 27 ASP n 1 28 ASN n 1 29 LYS n 1 30 VAL n 1 31 ALA n 1 32 MSE n 1 33 ALA n 1 34 LYS n 1 35 MSE n 1 36 GLU n 1 37 THR n 1 38 ASP n 1 39 TRP n 1 40 PHE n 1 41 ASP n 1 42 LYS n 1 43 SER n 1 44 TYR n 1 45 ASP n 1 46 VAL n 1 47 ILE n 1 48 PHE n 1 49 THR n 1 50 ASN n 1 51 GLY n 1 52 ASP n 1 53 LYS n 1 54 LEU n 1 55 GLU n 1 56 PHE n 1 57 ASP n 1 58 LYS n 1 59 LYS n 1 60 GLY n 1 61 ILE n 1 62 TRP n 1 63 THR n 1 64 GLU n 1 65 VAL n 1 66 ASN n 1 67 CYS n 1 68 LYS n 1 69 TYR n 1 70 SER n 1 71 ALA n 1 72 VAL n 1 73 PRO n 1 74 VAL n 1 75 ALA n 1 76 VAL n 1 77 VAL n 1 78 PRO n 1 79 ASP n 1 80 ALA n 1 81 ILE n 1 82 LYS n 1 83 LYS n 1 84 TYR n 1 85 VAL n 1 86 ALA n 1 87 THR n 1 88 ASN n 1 89 TYR n 1 90 PRO n 1 91 ASP n 1 92 ALA n 1 93 LYS n 1 94 MSE n 1 95 LEU n 1 96 LYS n 1 97 ILE n 1 98 GLU n 1 99 ARG n 1 100 ASP n 1 101 LYS n 1 102 HIS n 1 103 ASP n 1 104 TYR n 1 105 GLU n 1 106 VAL n 1 107 LYS n 1 108 LEU n 1 109 SER n 1 110 ASN n 1 111 GLY n 1 112 TRP n 1 113 GLU n 1 114 ILE n 1 115 LYS n 1 116 PHE n 1 117 ASP n 1 118 MSE n 1 119 GLN n 1 120 PHE n 1 121 ASN n 1 122 VAL n 1 123 ILE n 1 124 ASP n 1 125 ILE n 1 126 ASP n 1 127 ASN 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 'YP_001300247.1, BVU_2987' _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 'Bacteroides vulgatus ATCC 8482' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 435590 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 8482 _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain HK100 _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 SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A6L4L1_BACV8 _struct_ref.pdbx_db_accession A6L4L1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ADDDKPIQVNQLPQTAQTFIKTHFPDNKVAMAKMETDWFDKSYDVIFTNGDKLEFDKKGIWTEVNCKYSAVPVAVVPDAI KKYVATNYPDAKMLKIERDKHDYEVKLSNGWEIKFDMQFNVIDIDN ; _struct_ref.pdbx_align_begin 20 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DUE _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 127 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A6L4L1 _struct_ref_seq.db_align_beg 20 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 145 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 20 _struct_ref_seq.pdbx_auth_seq_align_end 145 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3DUE _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code A6L4L1 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 CAC non-polymer . 'CACODYLATE ION' dimethylarsinate 'C2 H6 As O2 -1' 136.989 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 3DUE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.69 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '35.0000% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date 2008-06-15 _diffrn_detector.details 'Flat mirror (vertical focusing)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91837 1.0 2 0.97926 1.0 3 0.97876 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.91837,0.97926,0.97876 # _reflns.entry_id 3DUE _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.361 _reflns.d_resolution_high 1.85 _reflns.number_obs 11519 _reflns.number_all ? _reflns.percent_possible_obs 100.000 _reflns.pdbx_Rmerge_I_obs 0.109 _reflns.pdbx_Rsym_value 0.109 _reflns.pdbx_netI_over_sigmaI 5.400 _reflns.B_iso_Wilson_estimate 17.91 _reflns.pdbx_redundancy 3.500 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _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 _reflns_shell.pdbx_diffrn_id 1.85 1.90 100.00 0.588 0.588 1.3 3.60 ? ? ? ? ? ? 1 1 1.90 1.95 100.00 0.447 0.447 1.7 3.60 ? ? ? ? ? ? 2 1 1.95 2.01 100.00 0.380 0.380 2.0 3.60 ? ? ? ? ? ? 3 1 2.01 2.07 100.00 0.294 0.294 2.6 3.60 ? ? ? ? ? ? 4 1 2.07 2.14 100.00 0.255 0.255 3.0 3.60 ? ? ? ? ? ? 5 1 2.14 2.21 100.00 0.222 0.222 3.4 3.60 ? ? ? ? ? ? 6 1 2.21 2.29 100.00 0.203 0.203 3.5 3.60 ? ? ? ? ? ? 7 1 2.29 2.39 100.00 0.175 0.175 4.3 3.60 ? ? ? ? ? ? 8 1 2.39 2.49 100.00 0.167 0.167 4.5 3.60 ? ? ? ? ? ? 9 1 2.49 2.62 100.00 0.135 0.135 5.4 3.60 ? ? ? ? ? ? 10 1 2.62 2.76 100.00 0.128 0.128 5.3 3.60 ? ? ? ? ? ? 11 1 2.76 2.93 100.00 0.109 0.109 6.3 3.60 ? ? ? ? ? ? 12 1 2.93 3.13 100.00 0.096 0.096 6.9 3.50 ? ? ? ? ? ? 13 1 3.13 3.38 100.00 0.077 0.077 8.0 3.50 ? ? ? ? ? ? 14 1 3.38 3.70 100.00 0.066 0.066 8.0 3.50 ? ? ? ? ? ? 15 1 3.70 4.14 100.00 0.052 0.052 11.8 3.50 ? ? ? ? ? ? 16 1 4.14 4.78 100.00 0.057 0.057 10.5 3.40 ? ? ? ? ? ? 17 1 4.78 5.85 100.00 0.069 0.069 8.5 3.40 ? ? ? ? ? ? 18 1 5.85 8.27 100.00 0.064 0.064 10.3 3.20 ? ? ? ? ? ? 19 1 8.27 29.37 97.10 0.052 0.052 10.9 2.80 ? ? ? ? ? ? 20 1 # _refine.entry_id 3DUE _refine.ls_number_reflns_obs 10931 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.361 _refine.ls_d_res_high 1.85 _refine.ls_percent_reflns_obs 99.96 _refine.ls_R_factor_obs 0.19432 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19234 _refine.ls_R_factor_R_free 0.23321 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 549 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.932 _refine.B_iso_mean 19.076 _refine.aniso_B[1][1] -0.71 _refine.aniso_B[2][2] 0.68 _refine.aniso_B[3][3] 0.03 _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 MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORAT 4. THE CACODYLATE MOLECULE WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS AND IS SUPPORTED BY AN ANOMALOUS DIFFERENCE FOURIER MAP CALCULATED AT THIS WAVELENGTH. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.158 _refine.pdbx_overall_ESU_R_Free 0.144 _refine.overall_SU_ML 0.100 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 6.130 _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_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 1019 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 133 _refine_hist.number_atoms_total 1157 _refine_hist.d_res_high 1.85 _refine_hist.d_res_low 29.361 # 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 0.015 0.022 ? 1070 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 693 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.654 1.934 ? 1460 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.940 3.000 ? 1710 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.367 5.000 ? 132 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38.168 26.364 ? 55 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 10.880 15.000 ? 180 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 5.690 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.106 0.200 ? 158 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 1199 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 203 'X-RAY DIFFRACTION' ? r_nbd_refined 0.212 0.200 ? 192 'X-RAY DIFFRACTION' ? r_nbd_other 0.193 0.200 ? 667 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.184 0.200 ? 519 'X-RAY DIFFRACTION' ? r_nbtor_other 0.089 0.200 ? 512 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.194 0.200 ? 95 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other 0.335 0.200 ? 1 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.250 0.200 ? 17 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.244 0.200 ? 24 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.204 0.200 ? 19 '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 1.422 2.000 ? 665 'X-RAY DIFFRACTION' ? r_mcbond_other 0.343 2.000 ? 254 'X-RAY DIFFRACTION' ? r_mcangle_it 1.964 3.000 ? 1056 'X-RAY DIFFRACTION' ? r_scbond_it 1.502 2.000 ? 475 'X-RAY DIFFRACTION' ? r_scangle_it 2.237 3.000 ? 401 '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 1.850 _refine_ls_shell.d_res_low 1.898 _refine_ls_shell.number_reflns_R_work 789 _refine_ls_shell.R_factor_R_work 0.218 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.401 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 40 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3DUE _struct.title ;CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;PUTATIVE PERIPLASMIC PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, UNKNOWN FUNCTION ; _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.entry_id 3DUE # 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 _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 9 ? LEU A 13 ? GLN A 27 LEU A 31 5 ? 5 HELX_P HELX_P2 2 PRO A 14 ? PHE A 25 ? PRO A 32 PHE A 43 1 ? 12 HELX_P HELX_P3 3 PRO A 73 ? VAL A 77 ? PRO A 91 VAL A 95 5 ? 5 HELX_P HELX_P4 4 PRO A 78 ? TYR A 89 ? PRO A 96 TYR A 107 1 ? 12 # _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 ALA 31 C ? ? ? 1_555 A MSE 32 N ? ? A ALA 49 A MSE 50 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale2 covale both ? A MSE 32 C ? ? ? 1_555 A ALA 33 N ? ? A MSE 50 A ALA 51 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale3 covale both ? A LYS 34 C ? ? ? 1_555 A MSE 35 N ? ? A LYS 52 A MSE 53 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale4 covale both ? A MSE 35 C ? ? ? 1_555 A GLU 36 N ? ? A MSE 53 A GLU 54 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale5 covale both ? A LYS 93 C ? ? ? 1_555 A MSE 94 N ? ? A LYS 111 A MSE 112 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale6 covale both ? A MSE 94 C ? ? ? 1_555 A LEU 95 N ? ? A MSE 112 A LEU 113 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? A ASP 117 C ? ? ? 1_555 A MSE 118 N ? ? A ASP 135 A MSE 136 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale8 covale both ? A MSE 118 C ? ? ? 1_555 A GLN 119 N ? ? A MSE 136 A GLN 137 1_555 ? ? ? ? ? ? ? 1.322 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 9 _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 # 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 LYS A 6 ? PRO A 7 ? LYS A 24 PRO A 25 A 2 VAL A 30 ? ASP A 38 ? VAL A 48 ASP A 56 A 3 ASP A 41 ? PHE A 48 ? ASP A 59 PHE A 66 A 4 LYS A 53 ? PHE A 56 ? LYS A 71 PHE A 74 A 5 TRP A 62 ? ASN A 66 ? TRP A 80 ASN A 84 A 6 MSE A 94 ? ARG A 99 ? MSE A 112 ARG A 117 A 7 ASP A 103 ? LEU A 108 ? ASP A 121 LEU A 126 A 8 GLU A 113 ? ASP A 117 ? GLU A 131 ASP A 135 A 9 VAL A 122 ? ASP A 126 ? VAL A 140 ASP A 144 # 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 LYS A 6 ? N LYS A 24 O MSE A 35 ? O MSE A 53 A 2 3 N GLU A 36 ? N GLU A 54 O SER A 43 ? O SER A 61 A 3 4 N VAL A 46 ? N VAL A 64 O LEU A 54 ? O LEU A 72 A 4 5 N LYS A 53 ? N LYS A 71 O ASN A 66 ? O ASN A 84 A 5 6 N VAL A 65 ? N VAL A 83 O ILE A 97 ? O ILE A 115 A 6 7 N LYS A 96 ? N LYS A 114 O LYS A 107 ? O LYS A 125 A 7 8 N VAL A 106 ? N VAL A 124 O ILE A 114 ? O ILE A 132 A 8 9 N GLU A 113 ? N GLU A 131 O ASP A 126 ? O ASP A 144 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id CAC _struct_site.pdbx_auth_seq_id 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 7 _struct_site.details 'BINDING SITE FOR RESIDUE CAC 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 7 GLY A 1 ? GLY A 0 . ? 4_565 ? 2 AC1 7 ASP A 38 ? ASP A 56 . ? 4_565 ? 3 AC1 7 TRP A 39 ? TRP A 57 . ? 4_565 ? 4 AC1 7 GLY A 51 ? GLY A 69 . ? 1_555 ? 5 AC1 7 LYS A 68 ? LYS A 86 . ? 1_555 ? 6 AC1 7 TYR A 69 ? TYR A 87 . ? 1_555 ? 7 AC1 7 HOH C . ? HOH A 251 . ? 4_565 ? # _atom_sites.entry_id 3DUE _atom_sites.fract_transf_matrix[1][1] 0.031645 _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] 0.019656 _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] 0.012578 _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 AS C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 0 GLY GLY A . n A 1 2 ALA 2 20 20 ALA ALA A . n A 1 3 ASP 3 21 21 ASP ASP A . n A 1 4 ASP 4 22 22 ASP ASP A . n A 1 5 ASP 5 23 23 ASP ASP A . n A 1 6 LYS 6 24 24 LYS LYS A . n A 1 7 PRO 7 25 25 PRO PRO A . n A 1 8 ILE 8 26 26 ILE ILE A . n A 1 9 GLN 9 27 27 GLN GLN A . n A 1 10 VAL 10 28 28 VAL VAL A . n A 1 11 ASN 11 29 29 ASN ASN A . n A 1 12 GLN 12 30 30 GLN GLN A . n A 1 13 LEU 13 31 31 LEU LEU A . n A 1 14 PRO 14 32 32 PRO PRO A . n A 1 15 GLN 15 33 33 GLN GLN A . n A 1 16 THR 16 34 34 THR THR A . n A 1 17 ALA 17 35 35 ALA ALA A . n A 1 18 GLN 18 36 36 GLN GLN A . n A 1 19 THR 19 37 37 THR THR A . n A 1 20 PHE 20 38 38 PHE PHE A . n A 1 21 ILE 21 39 39 ILE ILE A . n A 1 22 LYS 22 40 40 LYS LYS A . n A 1 23 THR 23 41 41 THR THR A . n A 1 24 HIS 24 42 42 HIS HIS A . n A 1 25 PHE 25 43 43 PHE PHE A . n A 1 26 PRO 26 44 44 PRO PRO A . n A 1 27 ASP 27 45 45 ASP ASP A . n A 1 28 ASN 28 46 46 ASN ASN A . n A 1 29 LYS 29 47 47 LYS LYS A . n A 1 30 VAL 30 48 48 VAL VAL A . n A 1 31 ALA 31 49 49 ALA ALA A . n A 1 32 MSE 32 50 50 MSE MSE A . n A 1 33 ALA 33 51 51 ALA ALA A . n A 1 34 LYS 34 52 52 LYS LYS A . n A 1 35 MSE 35 53 53 MSE MSE A . n A 1 36 GLU 36 54 54 GLU GLU A . n A 1 37 THR 37 55 55 THR THR A . n A 1 38 ASP 38 56 56 ASP ASP A . n A 1 39 TRP 39 57 57 TRP TRP A . n A 1 40 PHE 40 58 58 PHE PHE A . n A 1 41 ASP 41 59 59 ASP ASP A . n A 1 42 LYS 42 60 60 LYS LYS A . n A 1 43 SER 43 61 61 SER SER A . n A 1 44 TYR 44 62 62 TYR TYR A . n A 1 45 ASP 45 63 63 ASP ASP A . n A 1 46 VAL 46 64 64 VAL VAL A . n A 1 47 ILE 47 65 65 ILE ILE A . n A 1 48 PHE 48 66 66 PHE PHE A . n A 1 49 THR 49 67 67 THR THR A . n A 1 50 ASN 50 68 68 ASN ASN A . n A 1 51 GLY 51 69 69 GLY GLY A . n A 1 52 ASP 52 70 70 ASP ASP A . n A 1 53 LYS 53 71 71 LYS LYS A . n A 1 54 LEU 54 72 72 LEU LEU A . n A 1 55 GLU 55 73 73 GLU GLU A . n A 1 56 PHE 56 74 74 PHE PHE A . n A 1 57 ASP 57 75 75 ASP ASP A . n A 1 58 LYS 58 76 76 LYS LYS A . n A 1 59 LYS 59 77 77 LYS LYS A . n A 1 60 GLY 60 78 78 GLY GLY A . n A 1 61 ILE 61 79 79 ILE ILE A . n A 1 62 TRP 62 80 80 TRP TRP A . n A 1 63 THR 63 81 81 THR THR A . n A 1 64 GLU 64 82 82 GLU GLU A . n A 1 65 VAL 65 83 83 VAL VAL A . n A 1 66 ASN 66 84 84 ASN ASN A . n A 1 67 CYS 67 85 85 CYS CYS A . n A 1 68 LYS 68 86 86 LYS LYS A . n A 1 69 TYR 69 87 87 TYR TYR A . n A 1 70 SER 70 88 88 SER SER A . n A 1 71 ALA 71 89 89 ALA ALA A . n A 1 72 VAL 72 90 90 VAL VAL A . n A 1 73 PRO 73 91 91 PRO PRO A . n A 1 74 VAL 74 92 92 VAL VAL A . n A 1 75 ALA 75 93 93 ALA ALA A . n A 1 76 VAL 76 94 94 VAL VAL A . n A 1 77 VAL 77 95 95 VAL VAL A . n A 1 78 PRO 78 96 96 PRO PRO A . n A 1 79 ASP 79 97 97 ASP ASP A . n A 1 80 ALA 80 98 98 ALA ALA A . n A 1 81 ILE 81 99 99 ILE ILE A . n A 1 82 LYS 82 100 100 LYS LYS A . n A 1 83 LYS 83 101 101 LYS LYS A . n A 1 84 TYR 84 102 102 TYR TYR A . n A 1 85 VAL 85 103 103 VAL VAL A . n A 1 86 ALA 86 104 104 ALA ALA A . n A 1 87 THR 87 105 105 THR THR A . n A 1 88 ASN 88 106 106 ASN ASN A . n A 1 89 TYR 89 107 107 TYR TYR A . n A 1 90 PRO 90 108 108 PRO PRO A . n A 1 91 ASP 91 109 109 ASP ASP A . n A 1 92 ALA 92 110 110 ALA ALA A . n A 1 93 LYS 93 111 111 LYS LYS A . n A 1 94 MSE 94 112 112 MSE MSE A . n A 1 95 LEU 95 113 113 LEU LEU A . n A 1 96 LYS 96 114 114 LYS LYS A . n A 1 97 ILE 97 115 115 ILE ILE A . n A 1 98 GLU 98 116 116 GLU GLU A . n A 1 99 ARG 99 117 117 ARG ARG A . n A 1 100 ASP 100 118 118 ASP ASP A . n A 1 101 LYS 101 119 119 LYS LYS A . n A 1 102 HIS 102 120 120 HIS HIS A . n A 1 103 ASP 103 121 121 ASP ASP A . n A 1 104 TYR 104 122 122 TYR TYR A . n A 1 105 GLU 105 123 123 GLU GLU A . n A 1 106 VAL 106 124 124 VAL VAL A . n A 1 107 LYS 107 125 125 LYS LYS A . n A 1 108 LEU 108 126 126 LEU LEU A . n A 1 109 SER 109 127 127 SER SER A . n A 1 110 ASN 110 128 128 ASN ASN A . n A 1 111 GLY 111 129 129 GLY GLY A . n A 1 112 TRP 112 130 130 TRP TRP A . n A 1 113 GLU 113 131 131 GLU GLU A . n A 1 114 ILE 114 132 132 ILE ILE A . n A 1 115 LYS 115 133 133 LYS LYS A . n A 1 116 PHE 116 134 134 PHE PHE A . n A 1 117 ASP 117 135 135 ASP ASP A . n A 1 118 MSE 118 136 136 MSE MSE A . n A 1 119 GLN 119 137 137 GLN GLN A . n A 1 120 PHE 120 138 138 PHE PHE A . n A 1 121 ASN 121 139 139 ASN ASN A . n A 1 122 VAL 122 140 140 VAL VAL A . n A 1 123 ILE 123 141 141 ILE ILE A . n A 1 124 ASP 124 142 142 ASP ASP A . n A 1 125 ILE 125 143 143 ILE ILE A . n A 1 126 ASP 126 144 144 ASP ASP A . n A 1 127 ASN 127 145 145 ASN ASN A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # 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 CAC 1 1 1 CAC CAC A . C 3 HOH 1 146 2 HOH HOH A . C 3 HOH 2 147 3 HOH HOH A . C 3 HOH 3 148 4 HOH HOH A . C 3 HOH 4 149 5 HOH HOH A . C 3 HOH 5 150 6 HOH HOH A . C 3 HOH 6 151 7 HOH HOH A . C 3 HOH 7 152 8 HOH HOH A . C 3 HOH 8 153 9 HOH HOH A . C 3 HOH 9 154 10 HOH HOH A . C 3 HOH 10 155 11 HOH HOH A . C 3 HOH 11 156 12 HOH HOH A . C 3 HOH 12 157 13 HOH HOH A . C 3 HOH 13 158 14 HOH HOH A . C 3 HOH 14 159 15 HOH HOH A . C 3 HOH 15 160 16 HOH HOH A . C 3 HOH 16 161 17 HOH HOH A . C 3 HOH 17 162 18 HOH HOH A . C 3 HOH 18 163 19 HOH HOH A . C 3 HOH 19 164 20 HOH HOH A . C 3 HOH 20 165 21 HOH HOH A . C 3 HOH 21 166 22 HOH HOH A . C 3 HOH 22 167 23 HOH HOH A . C 3 HOH 23 168 24 HOH HOH A . C 3 HOH 24 169 25 HOH HOH A . C 3 HOH 25 170 26 HOH HOH A . C 3 HOH 26 171 27 HOH HOH A . C 3 HOH 27 172 28 HOH HOH A . C 3 HOH 28 173 29 HOH HOH A . C 3 HOH 29 174 30 HOH HOH A . C 3 HOH 30 175 31 HOH HOH A . C 3 HOH 31 176 32 HOH HOH A . C 3 HOH 32 177 33 HOH HOH A . C 3 HOH 33 178 34 HOH HOH A . C 3 HOH 34 179 35 HOH HOH A . C 3 HOH 35 180 36 HOH HOH A . C 3 HOH 36 181 37 HOH HOH A . C 3 HOH 37 182 38 HOH HOH A . C 3 HOH 38 183 39 HOH HOH A . C 3 HOH 39 184 40 HOH HOH A . C 3 HOH 40 185 41 HOH HOH A . C 3 HOH 41 186 42 HOH HOH A . C 3 HOH 42 187 43 HOH HOH A . C 3 HOH 43 188 44 HOH HOH A . C 3 HOH 44 189 45 HOH HOH A . C 3 HOH 45 190 46 HOH HOH A . C 3 HOH 46 191 47 HOH HOH A . C 3 HOH 47 192 48 HOH HOH A . C 3 HOH 48 193 49 HOH HOH A . C 3 HOH 49 194 50 HOH HOH A . C 3 HOH 50 195 51 HOH HOH A . C 3 HOH 51 196 52 HOH HOH A . C 3 HOH 52 197 53 HOH HOH A . C 3 HOH 53 198 54 HOH HOH A . C 3 HOH 54 199 55 HOH HOH A . C 3 HOH 55 200 56 HOH HOH A . C 3 HOH 56 201 57 HOH HOH A . C 3 HOH 57 202 58 HOH HOH A . C 3 HOH 58 203 59 HOH HOH A . C 3 HOH 59 204 60 HOH HOH A . C 3 HOH 60 205 61 HOH HOH A . C 3 HOH 61 206 62 HOH HOH A . C 3 HOH 62 207 63 HOH HOH A . C 3 HOH 63 208 64 HOH HOH A . C 3 HOH 64 209 65 HOH HOH A . C 3 HOH 65 210 66 HOH HOH A . C 3 HOH 66 211 67 HOH HOH A . C 3 HOH 67 212 68 HOH HOH A . C 3 HOH 68 213 69 HOH HOH A . C 3 HOH 69 214 70 HOH HOH A . C 3 HOH 70 215 71 HOH HOH A . C 3 HOH 71 216 72 HOH HOH A . C 3 HOH 72 217 73 HOH HOH A . C 3 HOH 73 218 74 HOH HOH A . C 3 HOH 74 219 75 HOH HOH A . C 3 HOH 75 220 76 HOH HOH A . C 3 HOH 76 221 77 HOH HOH A . C 3 HOH 77 222 78 HOH HOH A . C 3 HOH 78 223 79 HOH HOH A . C 3 HOH 79 224 80 HOH HOH A . C 3 HOH 80 225 81 HOH HOH A . C 3 HOH 81 226 82 HOH HOH A . C 3 HOH 82 227 83 HOH HOH A . C 3 HOH 83 228 84 HOH HOH A . C 3 HOH 84 229 85 HOH HOH A . C 3 HOH 85 230 86 HOH HOH A . C 3 HOH 86 231 87 HOH HOH A . C 3 HOH 87 232 88 HOH HOH A . C 3 HOH 88 233 89 HOH HOH A . C 3 HOH 89 234 90 HOH HOH A . C 3 HOH 90 235 91 HOH HOH A . C 3 HOH 91 236 92 HOH HOH A . C 3 HOH 92 237 93 HOH HOH A . C 3 HOH 93 238 94 HOH HOH A . C 3 HOH 94 239 95 HOH HOH A . C 3 HOH 95 240 96 HOH HOH A . C 3 HOH 96 241 97 HOH HOH A . C 3 HOH 97 242 98 HOH HOH A . C 3 HOH 98 243 99 HOH HOH A . C 3 HOH 99 244 100 HOH HOH A . C 3 HOH 100 245 101 HOH HOH A . C 3 HOH 101 246 102 HOH HOH A . C 3 HOH 102 247 103 HOH HOH A . C 3 HOH 103 248 104 HOH HOH A . C 3 HOH 104 249 105 HOH HOH A . C 3 HOH 105 250 106 HOH HOH A . C 3 HOH 106 251 107 HOH HOH A . C 3 HOH 107 252 108 HOH HOH A . C 3 HOH 108 253 109 HOH HOH A . C 3 HOH 109 254 110 HOH HOH A . C 3 HOH 110 255 111 HOH HOH A . C 3 HOH 111 256 112 HOH HOH A . C 3 HOH 112 257 113 HOH HOH A . C 3 HOH 113 258 114 HOH HOH A . C 3 HOH 114 259 115 HOH HOH A . C 3 HOH 115 260 116 HOH HOH A . C 3 HOH 116 261 117 HOH HOH A . C 3 HOH 117 262 118 HOH HOH A . C 3 HOH 118 263 119 HOH HOH A . C 3 HOH 119 264 120 HOH HOH A . C 3 HOH 120 265 121 HOH HOH A . C 3 HOH 121 266 122 HOH HOH A . C 3 HOH 122 267 123 HOH HOH A . C 3 HOH 123 268 124 HOH HOH A . C 3 HOH 124 269 125 HOH HOH A . C 3 HOH 125 270 126 HOH HOH A . C 3 HOH 126 271 127 HOH HOH A . C 3 HOH 127 272 128 HOH HOH A . C 3 HOH 128 273 129 HOH HOH A . C 3 HOH 129 274 130 HOH HOH A . C 3 HOH 130 275 131 HOH HOH A . C 3 HOH 131 276 132 HOH HOH A . C 3 HOH 132 277 133 HOH HOH A . C 3 HOH 133 278 134 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 32 A MSE 50 ? MET SELENOMETHIONINE 2 A MSE 35 A MSE 53 ? MET SELENOMETHIONINE 3 A MSE 94 A MSE 112 ? MET SELENOMETHIONINE 4 A MSE 118 A MSE 136 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,C # _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 2008-08-05 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2023-02-01 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' # 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' software 3 4 'Structure model' struct_conn 4 5 'Structure model' database_2 5 5 'Structure model' struct_ref_seq_dif 6 5 '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.name' 3 4 'Structure model' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 9.6413 _pdbx_refine_tls.origin_y 49.8873 _pdbx_refine_tls.origin_z 7.6608 _pdbx_refine_tls.T[1][1] -0.1253 _pdbx_refine_tls.T[2][2] -0.1413 _pdbx_refine_tls.T[3][3] -0.1046 _pdbx_refine_tls.T[1][2] 0.0031 _pdbx_refine_tls.T[1][3] 0.0340 _pdbx_refine_tls.T[2][3] 0.0117 _pdbx_refine_tls.L[1][1] 1.4798 _pdbx_refine_tls.L[2][2] 0.9561 _pdbx_refine_tls.L[3][3] 2.9269 _pdbx_refine_tls.L[1][2] 0.0635 _pdbx_refine_tls.L[1][3] 0.2355 _pdbx_refine_tls.L[2][3] 0.1531 _pdbx_refine_tls.S[1][1] 0.0455 _pdbx_refine_tls.S[1][2] -0.1466 _pdbx_refine_tls.S[1][3] -0.0150 _pdbx_refine_tls.S[2][1] 0.1258 _pdbx_refine_tls.S[2][2] -0.0034 _pdbx_refine_tls.S[2][3] 0.0475 _pdbx_refine_tls.S[3][1] 0.0682 _pdbx_refine_tls.S[3][2] 0.0335 _pdbx_refine_tls.S[3][3] -0.0421 _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 0 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 1 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 145 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 127 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _phasing.method MAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran_77 ? 5 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 autoSHARP . ? ? ? ? phasing ? ? ? 9 # _pdbx_entry_details.entry_id 3DUE _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT (RESIDUES 20-145) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OD2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ASP _pdbx_validate_close_contact.auth_seq_id_1 45 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 217 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # 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 TRP A 57 ? ? 51.77 -126.11 2 1 CYS A 85 ? ? -103.99 47.59 3 1 SER A 88 ? ? -148.15 -109.80 4 1 ASP A 118 ? ? -126.07 -155.91 # 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 LYS 40 ? CD ? A LYS 22 CD 2 1 Y 1 A LYS 40 ? CE ? A LYS 22 CE 3 1 Y 1 A LYS 40 ? NZ ? A LYS 22 NZ 4 1 Y 1 A LYS 47 ? CD ? A LYS 29 CD 5 1 Y 1 A LYS 47 ? CE ? A LYS 29 CE 6 1 Y 1 A LYS 47 ? NZ ? A LYS 29 NZ 7 1 Y 1 A LYS 101 ? CG ? A LYS 83 CG 8 1 Y 1 A LYS 101 ? CD ? A LYS 83 CD 9 1 Y 1 A LYS 101 ? CE ? A LYS 83 CE 10 1 Y 1 A LYS 101 ? NZ ? A LYS 83 NZ 11 1 Y 1 A LYS 119 ? CE ? A LYS 101 CE 12 1 Y 1 A LYS 119 ? NZ ? A LYS 101 NZ 13 1 Y 1 A LYS 125 ? CD ? A LYS 107 CD 14 1 Y 1 A LYS 125 ? CE ? A LYS 107 CE 15 1 Y 1 A LYS 125 ? NZ ? A LYS 107 NZ 16 1 Y 1 A ILE 143 ? CD1 ? A ILE 125 CD1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CACODYLATE ION' CAC 3 water HOH #