data_2PV4 # _entry.id 2PV4 # _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 2PV4 pdb_00002pv4 10.2210/pdb2pv4/pdb RCSB RCSB042806 ? ? WWPDB D_1000042806 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 373751 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2PV4 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-05-09 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _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 ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of uncharacterized protein (YP_928494.1) from Shewanella amazonensis SB2B at 1.95 A resolution' _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 ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 2PV4 _cell.length_a 35.957 _cell.length_b 47.283 _cell.length_c 98.695 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 2PV4 _symmetry.Int_Tables_number 19 _symmetry.space_group_name_H-M 'P 21 21 21' _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' 16577.127 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 2 ? ? ? ? 3 water nat water 18.015 71 ? ? ? ? # _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 ;G(MSE)SEIDANYRALAQQVADKVAGRVIALDRLPESLLTAYRSLCDELLADRDGRFTRAWDQLPDSASSLFERCVFHGF YLANAWIQLSIVARDISELQDTDEAIAEQEYSGLYVRVAEAALKESVKKLKKARTDRS(MSE)YNS(MSE)REV(MSE)G I ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSEIDANYRALAQQVADKVAGRVIALDRLPESLLTAYRSLCDELLADRDGRFTRAWDQLPDSASSLFERCVFHGFYLAN AWIQLSIVARDISELQDTDEAIAEQEYSGLYVRVAEAALKESVKKLKKARTDRSMYNSMREVMGI ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 373751 # 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 MSE n 1 3 SER n 1 4 GLU n 1 5 ILE n 1 6 ASP n 1 7 ALA n 1 8 ASN n 1 9 TYR n 1 10 ARG n 1 11 ALA n 1 12 LEU n 1 13 ALA n 1 14 GLN n 1 15 GLN n 1 16 VAL n 1 17 ALA n 1 18 ASP n 1 19 LYS n 1 20 VAL n 1 21 ALA n 1 22 GLY n 1 23 ARG n 1 24 VAL n 1 25 ILE n 1 26 ALA n 1 27 LEU n 1 28 ASP n 1 29 ARG n 1 30 LEU n 1 31 PRO n 1 32 GLU n 1 33 SER n 1 34 LEU n 1 35 LEU n 1 36 THR n 1 37 ALA n 1 38 TYR n 1 39 ARG n 1 40 SER n 1 41 LEU n 1 42 CYS n 1 43 ASP n 1 44 GLU n 1 45 LEU n 1 46 LEU n 1 47 ALA n 1 48 ASP n 1 49 ARG n 1 50 ASP n 1 51 GLY n 1 52 ARG n 1 53 PHE n 1 54 THR n 1 55 ARG n 1 56 ALA n 1 57 TRP n 1 58 ASP n 1 59 GLN n 1 60 LEU n 1 61 PRO n 1 62 ASP n 1 63 SER n 1 64 ALA n 1 65 SER n 1 66 SER n 1 67 LEU n 1 68 PHE n 1 69 GLU n 1 70 ARG n 1 71 CYS n 1 72 VAL n 1 73 PHE n 1 74 HIS n 1 75 GLY n 1 76 PHE n 1 77 TYR n 1 78 LEU n 1 79 ALA n 1 80 ASN n 1 81 ALA n 1 82 TRP n 1 83 ILE n 1 84 GLN n 1 85 LEU n 1 86 SER n 1 87 ILE n 1 88 VAL n 1 89 ALA n 1 90 ARG n 1 91 ASP n 1 92 ILE n 1 93 SER n 1 94 GLU n 1 95 LEU n 1 96 GLN n 1 97 ASP n 1 98 THR n 1 99 ASP n 1 100 GLU n 1 101 ALA n 1 102 ILE n 1 103 ALA n 1 104 GLU n 1 105 GLN n 1 106 GLU n 1 107 TYR n 1 108 SER n 1 109 GLY n 1 110 LEU n 1 111 TYR n 1 112 VAL n 1 113 ARG n 1 114 VAL n 1 115 ALA n 1 116 GLU n 1 117 ALA n 1 118 ALA n 1 119 LEU n 1 120 LYS n 1 121 GLU n 1 122 SER n 1 123 VAL n 1 124 LYS n 1 125 LYS n 1 126 LEU n 1 127 LYS n 1 128 LYS n 1 129 ALA n 1 130 ARG n 1 131 THR n 1 132 ASP n 1 133 ARG n 1 134 SER n 1 135 MSE n 1 136 TYR n 1 137 ASN n 1 138 SER n 1 139 MSE n 1 140 ARG n 1 141 GLU n 1 142 VAL n 1 143 MSE n 1 144 GLY n 1 145 ILE 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 Shewanella _entity_src_gen.pdbx_gene_src_gene 'YP_928494.1, Sama_2622' _entity_src_gen.gene_src_species 'Shewanella amazonensis' _entity_src_gen.gene_src_strain SB2B _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 'Shewanella amazonensis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 326297 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc BAA-1098 _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 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 A1S8W8_SHEAM _struct_ref.pdbx_db_accession A1S8W8 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSEIDANYRALAQQVADKVAGRVIALDRLPESLLTAYRSLCDELLADRDGRFTRAWDQLPDSASSLFERCVFHGFYLANA WIQLSIVARDISELQDTDEAIAEQEYSGLYVRVAEAALKESVKKLKKARTDRSMYNSMREVMGI ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2PV4 _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 145 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A1S8W8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 144 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 144 # 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 2PV4 GLY A 1 ? UNP A1S8W8 ? ? 'expression tag' 0 1 1 2PV4 MSE A 2 ? UNP A1S8W8 MET 1 'modified residue' 1 2 1 2PV4 MSE A 135 ? UNP A1S8W8 MET 134 'modified residue' 134 3 1 2PV4 MSE A 139 ? UNP A1S8W8 MET 138 'modified residue' 138 4 1 2PV4 MSE A 143 ? UNP A1S8W8 MET 142 'modified residue' 142 5 # 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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.method 'X-RAY DIFFRACTION' _exptl.entry_id 2PV4 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.53 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 51.39 _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 9.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details 'NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat collimating mirror, toroid focusing mirror' _diffrn_detector.pdbx_collection_date 2007-04-01 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double crystal' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91162 1.0 2 0.97936 1.0 3 0.97922 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL9-2 _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list '0.91162, 0.97936, 0.97922' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 2PV4 _reflns.d_resolution_high 1.95 _reflns.d_resolution_low 29.062 _reflns.number_obs 12889 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_netI_over_sigmaI 6.700 _reflns.pdbx_Rsym_value 0.069 _reflns.pdbx_redundancy 3.900 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate 35.56 _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.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 1.95 2.00 ? 3769 ? 0.604 1.3 0.604 ? 4.00 ? 942 100.00 1 1 2.00 2.06 ? 3654 ? 0.488 1.6 0.488 ? 4.00 ? 911 100.00 2 1 2.06 2.12 ? 3524 ? 0.383 1.9 0.383 ? 4.00 ? 884 100.00 3 1 2.12 2.18 ? 3417 ? 0.297 2.5 0.297 ? 4.00 ? 850 100.00 4 1 2.18 2.25 ? 3351 ? 0.258 2.7 0.258 ? 4.00 ? 847 100.00 5 1 2.25 2.33 ? 3156 ? 0.225 3.2 0.225 ? 4.00 ? 788 100.00 6 1 2.33 2.42 ? 3134 ? 0.152 4.8 0.152 ? 4.00 ? 786 100.00 7 1 2.42 2.52 ? 3024 ? 0.134 5.3 0.134 ? 4.00 ? 756 100.00 8 1 2.52 2.63 ? 2891 ? 0.115 6.1 0.115 ? 4.00 ? 728 100.00 9 1 2.63 2.76 ? 2770 ? 0.098 6.9 0.098 ? 3.90 ? 702 100.00 10 1 2.76 2.91 ? 2601 ? 0.091 7.1 0.091 ? 4.00 ? 654 100.00 11 1 2.91 3.08 ? 2476 ? 0.083 7.7 0.083 ? 3.90 ? 632 100.00 12 1 3.08 3.30 ? 2387 ? 0.070 8.8 0.070 ? 3.90 ? 611 100.00 13 1 3.30 3.56 ? 2139 ? 0.059 9.9 0.059 ? 3.90 ? 546 100.00 14 1 3.56 3.90 ? 2012 ? 0.051 12.0 0.051 ? 3.90 ? 518 100.00 15 1 3.90 4.36 ? 1825 ? 0.047 13.2 0.047 ? 3.80 ? 476 100.00 16 1 4.36 5.03 ? 1608 ? 0.052 11.5 0.052 ? 3.80 ? 425 100.00 17 1 5.03 6.17 ? 1335 ? 0.055 10.4 0.055 ? 3.60 ? 368 100.00 18 1 6.17 8.72 ? 1030 ? 0.042 14.1 0.042 ? 3.50 ? 292 99.90 19 1 8.72 29.06 ? 525 ? 0.035 18.4 0.035 ? 3.00 ? 173 95.20 20 1 # _refine.entry_id 2PV4 _refine.ls_d_res_high 1.950 _refine.ls_d_res_low 29.062 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.900 _refine.ls_number_reflns_obs 12845 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 62 WAS NOT MODELED. ; _refine.ls_R_factor_all 0.208 _refine.ls_R_factor_R_work 0.205 _refine.ls_R_factor_R_free 0.250 _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 627 _refine.B_iso_mean 33.368 _refine.aniso_B[1][1] 0.690 _refine.aniso_B[2][2] -0.180 _refine.aniso_B[3][3] -0.520 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.924 _refine.pdbx_overall_ESU_R 0.169 _refine.pdbx_overall_ESU_R_Free 0.158 _refine.overall_SU_ML 0.110 _refine.overall_SU_B 7.710 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_obs 0.208 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1106 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 1189 _refine_hist.d_res_high 1.950 _refine_hist.d_res_low 29.062 # 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 1196 0.016 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 811 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1622 1.351 1.968 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1969 1.007 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 156 4.934 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 53 35.727 23.774 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 206 15.178 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 11 12.233 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 182 0.098 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1370 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 250 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 305 0.220 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 830 0.182 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 615 0.179 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 607 0.090 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 44 0.173 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 14 0.200 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 34 0.225 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 9 0.177 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 789 2.210 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 305 0.547 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1212 3.475 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 476 5.572 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 410 7.654 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.950 _refine_ls_shell.d_res_low 2.001 _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 897 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.281 _refine_ls_shell.R_factor_R_free 0.374 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 46 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 943 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2PV4 _struct.title ;CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3069 FAMILY (SAMA_2622) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.95 A RESOLUTION ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text '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 2PV4 # 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 2 ? D 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 GLY A 1 ? ARG A 23 ? GLY A 0 ARG A 22 1 ? 23 HELX_P HELX_P2 2 ALA A 26 ? LEU A 30 ? ALA A 25 LEU A 29 5 ? 5 HELX_P HELX_P3 3 PRO A 31 ? ASP A 48 ? PRO A 30 ASP A 47 1 ? 18 HELX_P HELX_P4 4 GLY A 51 ? LEU A 60 ? GLY A 50 LEU A 59 1 ? 10 HELX_P HELX_P5 5 PRO A 61 ? SER A 66 ? PRO A 60 SER A 65 1 ? 6 HELX_P HELX_P6 6 GLU A 69 ? ALA A 89 ? GLU A 68 ALA A 88 1 ? 21 HELX_P HELX_P7 7 ASP A 91 ? THR A 98 ? ASP A 90 THR A 97 1 ? 8 HELX_P HELX_P8 8 ALA A 103 ? ALA A 117 ? ALA A 102 ALA A 116 1 ? 15 HELX_P HELX_P9 9 ALA A 117 ? ARG A 130 ? ALA A 116 ARG A 129 1 ? 14 HELX_P HELX_P10 10 ASP A 132 ? GLY A 144 ? ASP A 131 GLY A 143 1 ? 13 # _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 GLY 1 C ? ? ? 1_555 A MSE 2 N ? ? A GLY 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A SER 3 N ? ? A MSE 1 A SER 2 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale3 covale both ? A SER 134 C ? ? ? 1_555 A MSE 135 N ? ? A SER 133 A MSE 134 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale4 covale both ? A MSE 135 C ? ? ? 1_555 A TYR 136 N ? ? A MSE 134 A TYR 135 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale5 covale both ? A SER 138 C A ? ? 1_555 A MSE 139 N ? ? A SER 137 A MSE 138 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale6 covale both ? A SER 138 C B ? ? 1_555 A MSE 139 N ? ? A SER 137 A MSE 138 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale7 covale both ? A MSE 139 C ? ? ? 1_555 A ARG 140 N ? ? A MSE 138 A ARG 139 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale8 covale both ? A VAL 142 C ? ? ? 1_555 A MSE 143 N B ? A VAL 141 A MSE 142 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale9 covale both ? A VAL 142 C ? ? ? 1_555 A MSE 143 N A ? A VAL 141 A MSE 142 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale10 covale both ? A MSE 143 C B ? ? 1_555 A GLY 144 N ? ? A MSE 142 A GLY 143 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale11 covale both ? A MSE 143 C A ? ? 1_555 A GLY 144 N ? ? A MSE 142 A GLY 143 1_555 ? ? ? ? ? ? ? 1.336 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GOL 145 ? 4 'BINDING SITE FOR RESIDUE GOL A 145' AC2 Software A GOL 146 ? 3 'BINDING SITE FOR RESIDUE GOL A 146' # 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 ASP A 6 ? ASP A 5 . ? 1_555 ? 2 AC1 4 ARG A 10 ? ARG A 9 . ? 1_555 ? 3 AC1 4 ARG A 70 ? ARG A 69 . ? 1_555 ? 4 AC1 4 HOH D . ? HOH A 157 . ? 1_555 ? 5 AC2 3 PRO A 61 ? PRO A 60 . ? 1_555 ? 6 AC2 3 LYS A 127 ? LYS A 126 . ? 1_555 ? 7 AC2 3 ARG A 130 ? ARG A 129 . ? 1_555 ? # _atom_sites.entry_id 2PV4 _atom_sites.fract_transf_matrix[1][1] 0.02781 _atom_sites.fract_transf_matrix[1][2] 0.00000 _atom_sites.fract_transf_matrix[1][3] 0.00000 _atom_sites.fract_transf_matrix[2][1] 0.00000 _atom_sites.fract_transf_matrix[2][2] 0.02115 _atom_sites.fract_transf_matrix[2][3] 0.00000 _atom_sites.fract_transf_matrix[3][1] 0.00000 _atom_sites.fract_transf_matrix[3][2] 0.00000 _atom_sites.fract_transf_matrix[3][3] 0.01013 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 0 GLY GLY A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 SER 3 2 2 SER SER A . n A 1 4 GLU 4 3 3 GLU GLU A . n A 1 5 ILE 5 4 4 ILE ILE A . n A 1 6 ASP 6 5 5 ASP ASP A . n A 1 7 ALA 7 6 6 ALA ALA A . n A 1 8 ASN 8 7 7 ASN ASN A . n A 1 9 TYR 9 8 8 TYR TYR A . n A 1 10 ARG 10 9 9 ARG ARG A . n A 1 11 ALA 11 10 10 ALA ALA A . n A 1 12 LEU 12 11 11 LEU LEU A . n A 1 13 ALA 13 12 12 ALA ALA A . n A 1 14 GLN 14 13 13 GLN GLN A . n A 1 15 GLN 15 14 14 GLN GLN A . n A 1 16 VAL 16 15 15 VAL VAL A . n A 1 17 ALA 17 16 16 ALA ALA A . n A 1 18 ASP 18 17 17 ASP ASP A . n A 1 19 LYS 19 18 18 LYS LYS A . n A 1 20 VAL 20 19 19 VAL VAL A . n A 1 21 ALA 21 20 20 ALA ALA A . n A 1 22 GLY 22 21 21 GLY GLY A . n A 1 23 ARG 23 22 22 ARG ARG A . n A 1 24 VAL 24 23 23 VAL VAL A . n A 1 25 ILE 25 24 24 ILE ILE A . n A 1 26 ALA 26 25 25 ALA ALA A . n A 1 27 LEU 27 26 26 LEU LEU A . n A 1 28 ASP 28 27 27 ASP ASP A . n A 1 29 ARG 29 28 28 ARG ARG A . n A 1 30 LEU 30 29 29 LEU LEU A . n A 1 31 PRO 31 30 30 PRO PRO A . n A 1 32 GLU 32 31 31 GLU GLU A . n A 1 33 SER 33 32 32 SER SER A . n A 1 34 LEU 34 33 33 LEU LEU A . n A 1 35 LEU 35 34 34 LEU LEU A . n A 1 36 THR 36 35 35 THR THR A . n A 1 37 ALA 37 36 36 ALA ALA A . n A 1 38 TYR 38 37 37 TYR TYR A . n A 1 39 ARG 39 38 38 ARG ARG A . n A 1 40 SER 40 39 39 SER SER A . n A 1 41 LEU 41 40 40 LEU LEU A . n A 1 42 CYS 42 41 41 CYS CYS A . n A 1 43 ASP 43 42 42 ASP ASP A . n A 1 44 GLU 44 43 43 GLU GLU A . n A 1 45 LEU 45 44 44 LEU LEU A . n A 1 46 LEU 46 45 45 LEU LEU A . n A 1 47 ALA 47 46 46 ALA ALA A . n A 1 48 ASP 48 47 47 ASP ASP A . n A 1 49 ARG 49 48 48 ARG ARG A . n A 1 50 ASP 50 49 49 ASP ASP A . n A 1 51 GLY 51 50 50 GLY GLY A . n A 1 52 ARG 52 51 51 ARG ARG A . n A 1 53 PHE 53 52 52 PHE PHE A . n A 1 54 THR 54 53 53 THR THR A . n A 1 55 ARG 55 54 54 ARG ARG A . n A 1 56 ALA 56 55 55 ALA ALA A . n A 1 57 TRP 57 56 56 TRP TRP A . n A 1 58 ASP 58 57 57 ASP ASP A . n A 1 59 GLN 59 58 58 GLN GLN A . n A 1 60 LEU 60 59 59 LEU LEU A . n A 1 61 PRO 61 60 60 PRO PRO A . n A 1 62 ASP 62 61 61 ASP ASP A . n A 1 63 SER 63 62 62 SER SER A . n A 1 64 ALA 64 63 63 ALA ALA A . n A 1 65 SER 65 64 64 SER SER A . n A 1 66 SER 66 65 65 SER SER A . n A 1 67 LEU 67 66 66 LEU LEU A . n A 1 68 PHE 68 67 67 PHE PHE A . n A 1 69 GLU 69 68 68 GLU GLU A . n A 1 70 ARG 70 69 69 ARG ARG A . n A 1 71 CYS 71 70 70 CYS CYS A . n A 1 72 VAL 72 71 71 VAL VAL A . n A 1 73 PHE 73 72 72 PHE PHE A . n A 1 74 HIS 74 73 73 HIS HIS A . n A 1 75 GLY 75 74 74 GLY GLY A . n A 1 76 PHE 76 75 75 PHE PHE A . n A 1 77 TYR 77 76 76 TYR TYR A . n A 1 78 LEU 78 77 77 LEU LEU A . n A 1 79 ALA 79 78 78 ALA ALA A . n A 1 80 ASN 80 79 79 ASN ASN A . n A 1 81 ALA 81 80 80 ALA ALA A . n A 1 82 TRP 82 81 81 TRP TRP A . n A 1 83 ILE 83 82 82 ILE ILE A . n A 1 84 GLN 84 83 83 GLN GLN A . n A 1 85 LEU 85 84 84 LEU LEU A . n A 1 86 SER 86 85 85 SER SER A . n A 1 87 ILE 87 86 86 ILE ILE A . n A 1 88 VAL 88 87 87 VAL VAL A . n A 1 89 ALA 89 88 88 ALA ALA A . n A 1 90 ARG 90 89 89 ARG ARG A . n A 1 91 ASP 91 90 90 ASP ASP A . n A 1 92 ILE 92 91 91 ILE ILE A . n A 1 93 SER 93 92 92 SER SER A . n A 1 94 GLU 94 93 93 GLU GLU A . n A 1 95 LEU 95 94 94 LEU LEU A . n A 1 96 GLN 96 95 95 GLN GLN A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 THR 98 97 97 THR THR A . n A 1 99 ASP 99 98 98 ASP ASP A . n A 1 100 GLU 100 99 99 GLU GLU A . n A 1 101 ALA 101 100 100 ALA ALA A . n A 1 102 ILE 102 101 101 ILE ILE A . n A 1 103 ALA 103 102 102 ALA ALA A . n A 1 104 GLU 104 103 103 GLU GLU A . n A 1 105 GLN 105 104 104 GLN GLN A . n A 1 106 GLU 106 105 105 GLU GLU A . n A 1 107 TYR 107 106 106 TYR TYR A . n A 1 108 SER 108 107 107 SER SER A . n A 1 109 GLY 109 108 108 GLY GLY A . n A 1 110 LEU 110 109 109 LEU LEU A . n A 1 111 TYR 111 110 110 TYR TYR A . n A 1 112 VAL 112 111 111 VAL VAL A . n A 1 113 ARG 113 112 112 ARG ARG A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 ALA 115 114 114 ALA ALA A . n A 1 116 GLU 116 115 115 GLU GLU A . n A 1 117 ALA 117 116 116 ALA ALA A . n A 1 118 ALA 118 117 117 ALA ALA A . n A 1 119 LEU 119 118 118 LEU LEU A . n A 1 120 LYS 120 119 119 LYS LYS A . n A 1 121 GLU 121 120 120 GLU GLU A . n A 1 122 SER 122 121 121 SER SER A . n A 1 123 VAL 123 122 122 VAL VAL A . n A 1 124 LYS 124 123 123 LYS LYS A . n A 1 125 LYS 125 124 124 LYS LYS A . n A 1 126 LEU 126 125 125 LEU LEU A . n A 1 127 LYS 127 126 126 LYS LYS A . n A 1 128 LYS 128 127 127 LYS LYS A . n A 1 129 ALA 129 128 128 ALA ALA A . n A 1 130 ARG 130 129 129 ARG ARG A . n A 1 131 THR 131 130 130 THR THR A . n A 1 132 ASP 132 131 131 ASP ASP A . n A 1 133 ARG 133 132 132 ARG ARG A . n A 1 134 SER 134 133 133 SER SER A . n A 1 135 MSE 135 134 134 MSE MSE A . n A 1 136 TYR 136 135 135 TYR TYR A . n A 1 137 ASN 137 136 136 ASN ASN A . n A 1 138 SER 138 137 137 SER SER A . n A 1 139 MSE 139 138 138 MSE MSE A . n A 1 140 ARG 140 139 139 ARG ARG A . n A 1 141 GLU 141 140 140 GLU GLU A . n A 1 142 VAL 142 141 141 VAL VAL A . n A 1 143 MSE 143 142 142 MSE MSE A . n A 1 144 GLY 144 143 143 GLY GLY A . n A 1 145 ILE 145 144 144 ILE ILE 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 GOL 1 145 1 GOL GOL A . C 2 GOL 1 146 2 GOL GOL A . D 3 HOH 1 147 3 HOH HOH A . D 3 HOH 2 148 4 HOH HOH A . D 3 HOH 3 149 5 HOH HOH A . D 3 HOH 4 150 6 HOH HOH A . D 3 HOH 5 151 7 HOH HOH A . D 3 HOH 6 152 8 HOH HOH A . D 3 HOH 7 153 9 HOH HOH A . D 3 HOH 8 154 10 HOH HOH A . D 3 HOH 9 155 11 HOH HOH A . D 3 HOH 10 156 12 HOH HOH A . D 3 HOH 11 157 13 HOH HOH A . D 3 HOH 12 158 14 HOH HOH A . D 3 HOH 13 159 15 HOH HOH A . D 3 HOH 14 160 16 HOH HOH A . D 3 HOH 15 161 17 HOH HOH A . D 3 HOH 16 162 18 HOH HOH A . D 3 HOH 17 163 19 HOH HOH A . D 3 HOH 18 164 20 HOH HOH A . D 3 HOH 19 165 21 HOH HOH A . D 3 HOH 20 166 22 HOH HOH A . D 3 HOH 21 167 23 HOH HOH A . D 3 HOH 22 168 24 HOH HOH A . D 3 HOH 23 169 25 HOH HOH A . D 3 HOH 24 170 26 HOH HOH A . D 3 HOH 25 171 27 HOH HOH A . D 3 HOH 26 172 28 HOH HOH A . D 3 HOH 27 173 29 HOH HOH A . D 3 HOH 28 174 30 HOH HOH A . D 3 HOH 29 175 31 HOH HOH A . D 3 HOH 30 176 32 HOH HOH A . D 3 HOH 31 177 33 HOH HOH A . D 3 HOH 32 178 34 HOH HOH A . D 3 HOH 33 179 35 HOH HOH A . D 3 HOH 34 180 36 HOH HOH A . D 3 HOH 35 181 37 HOH HOH A . D 3 HOH 36 182 38 HOH HOH A . D 3 HOH 37 183 39 HOH HOH A . D 3 HOH 38 184 40 HOH HOH A . D 3 HOH 39 185 41 HOH HOH A . D 3 HOH 40 186 42 HOH HOH A . D 3 HOH 41 187 43 HOH HOH A . D 3 HOH 42 188 44 HOH HOH A . D 3 HOH 43 189 45 HOH HOH A . D 3 HOH 44 190 46 HOH HOH A . D 3 HOH 45 191 47 HOH HOH A . D 3 HOH 46 192 48 HOH HOH A . D 3 HOH 47 193 49 HOH HOH A . D 3 HOH 48 194 50 HOH HOH A . D 3 HOH 49 195 51 HOH HOH A . D 3 HOH 50 196 52 HOH HOH A . D 3 HOH 51 197 53 HOH HOH A . D 3 HOH 52 198 54 HOH HOH A . D 3 HOH 53 199 55 HOH HOH A . D 3 HOH 54 200 56 HOH HOH A . D 3 HOH 55 201 57 HOH HOH A . D 3 HOH 56 202 58 HOH HOH A . D 3 HOH 57 203 59 HOH HOH A . D 3 HOH 58 204 60 HOH HOH A . D 3 HOH 59 205 61 HOH HOH A . D 3 HOH 60 206 62 HOH HOH A . D 3 HOH 61 207 63 HOH HOH A . D 3 HOH 62 208 64 HOH HOH A . D 3 HOH 63 209 65 HOH HOH A . D 3 HOH 64 210 66 HOH HOH A . D 3 HOH 65 211 67 HOH HOH A . D 3 HOH 66 212 68 HOH HOH A . D 3 HOH 67 213 69 HOH HOH A . D 3 HOH 68 214 70 HOH HOH A . D 3 HOH 69 215 71 HOH HOH A . D 3 HOH 70 216 72 HOH HOH A . D 3 HOH 71 217 73 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 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 135 A MSE 134 ? MET SELENOMETHIONINE 3 A MSE 139 A MSE 138 ? MET SELENOMETHIONINE 4 A MSE 143 A MSE 142 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 2007-05-22 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2023-01-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Source and taxonomy' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Database references' 7 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 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' struct_conn 4 5 'Structure model' struct_ref_seq_dif 5 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 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_struct_ref_seq_dif.details' 7 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 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 35.6117 _pdbx_refine_tls.origin_y 42.7980 _pdbx_refine_tls.origin_z 9.4737 _pdbx_refine_tls.T[1][1] -0.0728 _pdbx_refine_tls.T[2][2] -0.0644 _pdbx_refine_tls.T[3][3] -0.0283 _pdbx_refine_tls.T[1][2] 0.0079 _pdbx_refine_tls.T[1][3] -0.0091 _pdbx_refine_tls.T[2][3] -0.0534 _pdbx_refine_tls.L[1][1] 0.6516 _pdbx_refine_tls.L[2][2] 2.1066 _pdbx_refine_tls.L[3][3] 2.2875 _pdbx_refine_tls.L[1][2] 0.4619 _pdbx_refine_tls.L[1][3] 0.1160 _pdbx_refine_tls.L[2][3] 1.0406 _pdbx_refine_tls.S[1][1] 0.0088 _pdbx_refine_tls.S[2][2] -0.0984 _pdbx_refine_tls.S[3][3] 0.0896 _pdbx_refine_tls.S[1][2] 0.0320 _pdbx_refine_tls.S[1][3] -0.1561 _pdbx_refine_tls.S[2][3] 0.3315 _pdbx_refine_tls.S[2][1] -0.1444 _pdbx_refine_tls.S[3][1] -0.2922 _pdbx_refine_tls.S[3][2] -0.0537 _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_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 1 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 145 _pdbx_refine_tls_group.selection ALL _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 0 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 144 _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 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 1 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 2 REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran_77 ? 4 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 5 MAR345 CCD ? ? ? ? 'data collection' ? ? ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 SHARP . ? ? ? ? phasing ? ? ? 9 # loop_ _pdbx_database_remark.id _pdbx_database_remark.text 300 ; BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. ; 999 ; SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; # 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 MSE 1 ? CE ? A MSE 2 CE 2 1 Y 1 A SER 2 ? OG ? A SER 3 OG 3 1 Y 1 A GLU 31 ? CG ? A GLU 32 CG 4 1 Y 1 A GLU 31 ? CD ? A GLU 32 CD 5 1 Y 1 A GLU 31 ? OE1 ? A GLU 32 OE1 6 1 Y 1 A GLU 31 ? OE2 ? A GLU 32 OE2 7 1 Y 1 A SER 32 ? OG ? A SER 33 OG 8 1 Y 1 A ARG 38 ? NH1 ? A ARG 39 NH1 9 1 Y 1 A ARG 38 ? NH2 ? A ARG 39 NH2 10 1 Y 1 A ARG 54 ? CG ? A ARG 55 CG 11 1 Y 1 A ARG 54 ? CD ? A ARG 55 CD 12 1 Y 1 A ARG 54 ? NE ? A ARG 55 NE 13 1 Y 1 A ARG 54 ? CZ ? A ARG 55 CZ 14 1 Y 1 A ARG 54 ? NH1 ? A ARG 55 NH1 15 1 Y 1 A ARG 54 ? NH2 ? A ARG 55 NH2 16 1 Y 1 A GLN 58 ? OE1 ? A GLN 59 OE1 17 1 Y 1 A GLN 58 ? NE2 ? A GLN 59 NE2 18 1 Y 1 A ASP 90 ? OD1 ? A ASP 91 OD1 19 1 Y 1 A ASP 90 ? OD2 ? A ASP 91 OD2 20 1 Y 1 A ILE 91 ? CG1 ? A ILE 92 CG1 21 1 Y 1 A ILE 91 ? CG2 ? A ILE 92 CG2 22 1 Y 1 A ILE 91 ? CD1 ? A ILE 92 CD1 23 1 Y 1 A SER 92 ? OG ? A SER 93 OG 24 1 Y 1 A GLN 95 ? CG ? A GLN 96 CG 25 1 Y 1 A GLN 95 ? CD ? A GLN 96 CD 26 1 Y 1 A GLN 95 ? OE1 ? A GLN 96 OE1 27 1 Y 1 A GLN 95 ? NE2 ? A GLN 96 NE2 28 1 Y 1 A GLN 104 ? OE1 ? A GLN 105 OE1 29 1 Y 1 A GLN 104 ? NE2 ? A GLN 105 NE2 30 1 Y 1 A ARG 112 ? CZ ? A ARG 113 CZ 31 1 Y 1 A ARG 112 ? NH1 ? A ARG 113 NH1 32 1 Y 1 A ARG 112 ? NH2 ? A ARG 113 NH2 33 1 Y 1 A LYS 119 ? CE ? A LYS 120 CE 34 1 Y 1 A LYS 119 ? NZ ? A LYS 120 NZ 35 1 Y 1 A LYS 123 ? CD ? A LYS 124 CD 36 1 Y 1 A LYS 123 ? CE ? A LYS 124 CE 37 1 Y 1 A LYS 123 ? NZ ? A LYS 124 NZ 38 1 Y 1 A LYS 127 ? NZ ? A LYS 128 NZ 39 1 Y 1 A ARG 132 ? CZ ? A ARG 133 CZ 40 1 Y 1 A ARG 132 ? NH1 ? A ARG 133 NH1 41 1 Y 1 A ARG 132 ? NH2 ? A ARG 133 NH2 42 1 Y 1 A GLU 140 ? OE1 ? A GLU 141 OE1 43 1 Y 1 A GLU 140 ? OE2 ? A GLU 141 OE2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #