data_3RH2 # _entry.id 3RH2 # _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 3RH2 pdb_00003rh2 10.2210/pdb3rh2/pdb RCSB RCSB064922 ? ? WWPDB D_1000064922 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 399142 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3RH2 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-04-11 _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 ;Crystal structure of a Hypothetical TetR-like transcriptional regulator (Sama_0099) from SHEWANELLA AMAZONENSIS SB2B at 2.42 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 3RH2 _cell.length_a 123.536 _cell.length_b 123.536 _cell.length_c 49.552 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 3RH2 _symmetry.Int_Tables_number 96 _symmetry.space_group_name_H-M 'P 43 21 2' _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 'Hypothetical TetR-like transcriptional regulator' 25121.748 1 ? ? ? ? 2 non-polymer syn 'UNKNOWN LIGAND' ? 1 ? ? ? ? 3 non-polymer syn 'PHOSPHATE ION' 94.971 2 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 6 ? ? ? ? 5 water nat water 18.015 38 ? ? ? ? # _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)KTRDKIIQASLELFNEHGERTITTNHIAAHLDISPGNLYYHFRNKEDIIRCIFDQYEQHLLLGFKPYADQKVDL ELL(MSE)SYFDA(MSE)FYT(MSE)WQFRF(MSE)YANLADILARDDTLKARYLKVQQAVLEQSIAVLNQLKKDGILQI EDERIADLADTIK(MSE)IIGFWISYKLTQSSIATISKASLYEGLLRVL(MSE)IFKAYSTPDSLANFDRLEQHFRSQSN ; _entity_poly.pdbx_seq_one_letter_code_can ;GMKTRDKIIQASLELFNEHGERTITTNHIAAHLDISPGNLYYHFRNKEDIIRCIFDQYEQHLLLGFKPYADQKVDLELLM SYFDAMFYTMWQFRFMYANLADILARDDTLKARYLKVQQAVLEQSIAVLNQLKKDGILQIEDERIADLADTIKMIIGFWI SYKLTQSSIATISKASLYEGLLRVLMIFKAYSTPDSLANFDRLEQHFRSQSN ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 399142 # 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 LYS n 1 4 THR n 1 5 ARG n 1 6 ASP n 1 7 LYS n 1 8 ILE n 1 9 ILE n 1 10 GLN n 1 11 ALA n 1 12 SER n 1 13 LEU n 1 14 GLU n 1 15 LEU n 1 16 PHE n 1 17 ASN n 1 18 GLU n 1 19 HIS n 1 20 GLY n 1 21 GLU n 1 22 ARG n 1 23 THR n 1 24 ILE n 1 25 THR n 1 26 THR n 1 27 ASN n 1 28 HIS n 1 29 ILE n 1 30 ALA n 1 31 ALA n 1 32 HIS n 1 33 LEU n 1 34 ASP n 1 35 ILE n 1 36 SER n 1 37 PRO n 1 38 GLY n 1 39 ASN n 1 40 LEU n 1 41 TYR n 1 42 TYR n 1 43 HIS n 1 44 PHE n 1 45 ARG n 1 46 ASN n 1 47 LYS n 1 48 GLU n 1 49 ASP n 1 50 ILE n 1 51 ILE n 1 52 ARG n 1 53 CYS n 1 54 ILE n 1 55 PHE n 1 56 ASP n 1 57 GLN n 1 58 TYR n 1 59 GLU n 1 60 GLN n 1 61 HIS n 1 62 LEU n 1 63 LEU n 1 64 LEU n 1 65 GLY n 1 66 PHE n 1 67 LYS n 1 68 PRO n 1 69 TYR n 1 70 ALA n 1 71 ASP n 1 72 GLN n 1 73 LYS n 1 74 VAL n 1 75 ASP n 1 76 LEU n 1 77 GLU n 1 78 LEU n 1 79 LEU n 1 80 MSE n 1 81 SER n 1 82 TYR n 1 83 PHE n 1 84 ASP n 1 85 ALA n 1 86 MSE n 1 87 PHE n 1 88 TYR n 1 89 THR n 1 90 MSE n 1 91 TRP n 1 92 GLN n 1 93 PHE n 1 94 ARG n 1 95 PHE n 1 96 MSE n 1 97 TYR n 1 98 ALA n 1 99 ASN n 1 100 LEU n 1 101 ALA n 1 102 ASP n 1 103 ILE n 1 104 LEU n 1 105 ALA n 1 106 ARG n 1 107 ASP n 1 108 ASP n 1 109 THR n 1 110 LEU n 1 111 LYS n 1 112 ALA n 1 113 ARG n 1 114 TYR n 1 115 LEU n 1 116 LYS n 1 117 VAL n 1 118 GLN n 1 119 GLN n 1 120 ALA n 1 121 VAL n 1 122 LEU n 1 123 GLU n 1 124 GLN n 1 125 SER n 1 126 ILE n 1 127 ALA n 1 128 VAL n 1 129 LEU n 1 130 ASN n 1 131 GLN n 1 132 LEU n 1 133 LYS n 1 134 LYS n 1 135 ASP n 1 136 GLY n 1 137 ILE n 1 138 LEU n 1 139 GLN n 1 140 ILE n 1 141 GLU n 1 142 ASP n 1 143 GLU n 1 144 ARG n 1 145 ILE n 1 146 ALA n 1 147 ASP n 1 148 LEU n 1 149 ALA n 1 150 ASP n 1 151 THR n 1 152 ILE n 1 153 LYS n 1 154 MSE n 1 155 ILE n 1 156 ILE n 1 157 GLY n 1 158 PHE n 1 159 TRP n 1 160 ILE n 1 161 SER n 1 162 TYR n 1 163 LYS n 1 164 LEU n 1 165 THR n 1 166 GLN n 1 167 SER n 1 168 SER n 1 169 ILE n 1 170 ALA n 1 171 THR n 1 172 ILE n 1 173 SER n 1 174 LYS n 1 175 ALA n 1 176 SER n 1 177 LEU n 1 178 TYR n 1 179 GLU n 1 180 GLY n 1 181 LEU n 1 182 LEU n 1 183 ARG n 1 184 VAL n 1 185 LEU n 1 186 MSE n 1 187 ILE n 1 188 PHE n 1 189 LYS n 1 190 ALA n 1 191 TYR n 1 192 SER n 1 193 THR n 1 194 PRO n 1 195 ASP n 1 196 SER n 1 197 LEU n 1 198 ALA n 1 199 ASN n 1 200 PHE n 1 201 ASP n 1 202 ARG n 1 203 LEU n 1 204 GLU n 1 205 GLN n 1 206 HIS n 1 207 PHE n 1 208 ARG n 1 209 SER n 1 210 GLN n 1 211 SER n 1 212 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 Sama_0099 _entity_src_gen.gene_src_species ? _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 ? _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 A1S1Q5_SHEAM _struct_ref.pdbx_db_accession A1S1Q5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKTRDKIIQASLELFNEHGERTITTNHIAAHLDISPGNLYYHFRNKEDIIRCIFDQYEQHLLLGFKPYADQKVDLELLMS YFDAMFYTMWQFRFMYANLADILARDDTLKARYLKVQQAVLEQSIAVLNQLKKDGILQIEDERIADLADTIKMIIGFWIS YKLTQSSIATISKASLYEGLLRVLMIFKAYSTPDSLANFDRLEQHFRSQSN ; _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 3RH2 _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 212 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A1S1Q5 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 211 _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 211 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3RH2 _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 A1S1Q5 _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 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 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 PO4 non-polymer . 'PHOSPHATE ION' ? 'O4 P -3' 94.971 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 UNL non-polymer . 'UNKNOWN LIGAND' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3RH2 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.76 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 67.31 _exptl_crystal.description 'DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND ' _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 4.2 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '0.4M KH2PO4, 1.6M NaH2PO4, 0.1M Phosphate Citrate pH 4.2, NANODROP, 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 'double crystal monochromator' _diffrn_detector.pdbx_collection_date 2011-03-09 # _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 0.91837 1.0 2 0.97934 1.0 3 0.97915 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 0.91837,0.97934,0.97915 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3RH2 _reflns.d_resolution_high 2.42 _reflns.d_resolution_low 29.118 _reflns.number_obs 15161 _reflns.pdbx_Rmerge_I_obs 0.143 _reflns.pdbx_netI_over_sigmaI 7.820 _reflns.percent_possible_obs 99.700 _reflns.B_iso_Wilson_estimate 70.116 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # 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 2.420 2.510 16056 ? 2905 0.025 1.5 ? ? ? ? ? 99.800 1 1 2.510 2.610 15443 ? 2780 0.025 2.0 ? ? ? ? ? 99.600 2 1 2.610 2.720 14221 ? 2567 0.025 2.9 ? ? ? ? ? 99.800 3 1 2.720 2.870 16046 ? 2912 0.025 4.0 ? ? ? ? ? 99.700 4 1 2.870 3.050 15394 ? 2803 0.025 5.8 ? ? ? ? ? 99.900 5 1 3.050 3.280 14812 ? 2728 0.025 7.7 ? ? ? ? ? 99.900 6 1 3.280 3.610 14738 ? 2811 0.025 10.6 ? ? ? ? ? 99.800 7 1 3.610 4.130 14705 ? 2825 0.025 13.0 ? ? ? ? ? 99.900 8 1 4.130 5.190 14143 ? 2764 0.025 14.8 ? ? ? ? ? 99.900 9 1 5.190 ? 14833 ? 2822 0.025 15.8 ? ? ? ? ? 98.400 10 1 # _refine.entry_id 3RH2 _refine.ls_d_res_high 2.4200 _refine.ls_d_res_low 29.118 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.7400 _refine.ls_number_reflns_obs 15113 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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 INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE LIGAND-BINDING SITE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2068 _refine.ls_R_factor_R_work 0.2047 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2496 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.0000 _refine.ls_number_reflns_R_free 762 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 65.5524 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -2.0900 _refine.aniso_B[2][2] -2.0900 _refine.aniso_B[3][3] 4.1800 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9520 _refine.correlation_coeff_Fo_to_Fc_free 0.9180 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.2210 _refine.overall_SU_ML 0.1640 _refine.overall_SU_B 14.6800 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 132.460 _refine.B_iso_min 28.760 _refine.occupancy_max 1.000 _refine.occupancy_min 0.330 _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_overall_ESU_R ? _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 1720 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 54 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 1812 _refine_hist.d_res_high 2.4200 _refine_hist.d_res_low 29.118 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 1835 0.019 0.022 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 1258 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2477 1.724 1.967 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 3055 1.010 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 220 2.991 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 93 30.754 23.978 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 329 13.638 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 12 14.953 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 270 0.099 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1998 0.007 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 388 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 1064 2.067 3.000 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 428 0.475 3.000 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 1719 3.838 5.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 771 6.911 8.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 752 9.652 11.000 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.4200 _refine_ls_shell.d_res_low 2.4820 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.7200 _refine_ls_shell.number_reflns_R_work 1025 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3660 _refine_ls_shell.R_factor_R_free 0.4760 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 58 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1083 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3RH2 _struct.title 'Crystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;DNA/RNA-binding 3-helical bundle, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-Biology, DNA BINDING PROTEIN ; _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' _struct_keywords.entry_id 3RH2 # 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 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 5 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.' # 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 LYS A 3 ? GLY A 20 ? LYS A 2 GLY A 19 1 ? 18 HELX_P HELX_P2 2 GLU A 21 ? ILE A 24 ? GLU A 20 ILE A 23 5 ? 4 HELX_P HELX_P3 3 THR A 25 ? ASP A 34 ? THR A 24 ASP A 33 1 ? 10 HELX_P HELX_P4 4 SER A 36 ? PHE A 44 ? SER A 35 PHE A 43 1 ? 9 HELX_P HELX_P5 5 ASN A 46 ? PHE A 66 ? ASN A 45 PHE A 65 1 ? 21 HELX_P HELX_P6 6 ASP A 75 ? PHE A 93 ? ASP A 74 PHE A 92 1 ? 19 HELX_P HELX_P7 7 PHE A 93 ? ASN A 99 ? PHE A 92 ASN A 98 1 ? 7 HELX_P HELX_P8 8 ASN A 99 ? ARG A 106 ? ASN A 98 ARG A 105 1 ? 8 HELX_P HELX_P9 9 ASP A 107 ? ASP A 135 ? ASP A 106 ASP A 134 1 ? 29 HELX_P HELX_P10 10 GLU A 141 ? GLU A 143 ? GLU A 140 GLU A 142 5 ? 3 HELX_P HELX_P11 11 ARG A 144 ? SER A 167 ? ARG A 143 SER A 166 1 ? 24 HELX_P HELX_P12 12 SER A 173 ? ALA A 190 ? SER A 172 ALA A 189 1 ? 18 HELX_P HELX_P13 13 THR A 193 ? SER A 211 ? THR A 192 SER A 210 1 ? 19 # _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 MSE 2 C ? ? ? 1_555 A LYS 3 N ? ? A MSE 1 A LYS 2 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale2 covale both ? A LEU 79 C ? ? ? 1_555 A MSE 80 N ? ? A LEU 78 A MSE 79 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale3 covale both ? A MSE 80 C ? ? ? 1_555 A SER 81 N ? ? A MSE 79 A SER 80 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale4 covale both ? A ALA 85 C ? ? ? 1_555 A MSE 86 N ? ? A ALA 84 A MSE 85 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale5 covale both ? A MSE 86 C ? ? ? 1_555 A PHE 87 N ? ? A MSE 85 A PHE 86 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale6 covale both ? A THR 89 C ? ? ? 1_555 A MSE 90 N ? ? A THR 88 A MSE 89 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale7 covale both ? A MSE 90 C ? ? ? 1_555 A TRP 91 N ? ? A MSE 89 A TRP 90 1_555 ? ? ? ? ? ? ? 1.308 ? ? covale8 covale both ? A PHE 95 C ? ? ? 1_555 A MSE 96 N ? ? A PHE 94 A MSE 95 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale9 covale both ? A MSE 96 C ? ? ? 1_555 A TYR 97 N ? ? A MSE 95 A TYR 96 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale10 covale both ? A LYS 153 C ? ? ? 1_555 A MSE 154 N ? ? A LYS 152 A MSE 153 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale11 covale both ? A MSE 154 C ? ? ? 1_555 A ILE 155 N ? ? A MSE 153 A ILE 154 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale12 covale both ? A LEU 185 C ? ? ? 1_555 A MSE 186 N ? ? A LEU 184 A MSE 185 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale13 covale both ? A MSE 186 C ? ? ? 1_555 A ILE 187 N ? ? A MSE 185 A ILE 186 1_555 ? ? ? ? ? ? ? 1.347 ? ? # _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 PO4 302 ? 2 'BINDING SITE FOR RESIDUE PO4 A 302' AC2 Software A PO4 303 ? 2 'BINDING SITE FOR RESIDUE PO4 A 303' AC3 Software A GOL 304 ? 2 'BINDING SITE FOR RESIDUE GOL A 304' AC4 Software A GOL 305 ? 2 'BINDING SITE FOR RESIDUE GOL A 305' AC5 Software A GOL 306 ? 2 'BINDING SITE FOR RESIDUE GOL A 306' AC6 Software A GOL 307 ? 3 'BINDING SITE FOR RESIDUE GOL A 307' AC7 Software A GOL 308 ? 2 'BINDING SITE FOR RESIDUE GOL A 308' AC8 Software A GOL 309 ? 6 'BINDING SITE FOR RESIDUE GOL A 309' # 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 2 TYR A 42 ? TYR A 41 . ? 1_555 ? 2 AC1 2 HIS A 43 ? HIS A 42 . ? 1_555 ? 3 AC2 2 HIS A 206 ? HIS A 205 . ? 1_555 ? 4 AC2 2 HIS A 206 ? HIS A 205 . ? 7_555 ? 5 AC3 2 THR A 4 ? THR A 3 . ? 1_555 ? 6 AC3 2 GOL I . ? GOL A 308 . ? 1_555 ? 7 AC4 2 TRP A 91 ? TRP A 90 . ? 1_555 ? 8 AC4 2 LYS A 174 ? LYS A 173 . ? 1_555 ? 9 AC5 2 THR A 25 ? THR A 24 . ? 1_555 ? 10 AC5 2 ASN A 27 ? ASN A 26 . ? 1_555 ? 11 AC6 3 HIS A 28 ? HIS A 27 . ? 7_555 ? 12 AC6 3 HIS A 32 ? HIS A 31 . ? 1_555 ? 13 AC6 3 HIS A 32 ? HIS A 31 . ? 7_555 ? 14 AC7 2 TYR A 42 ? TYR A 41 . ? 1_555 ? 15 AC7 2 GOL E . ? GOL A 304 . ? 1_555 ? 16 AC8 6 LEU A 64 ? LEU A 63 . ? 1_555 ? 17 AC8 6 GLY A 65 ? GLY A 64 . ? 1_555 ? 18 AC8 6 LYS A 67 ? LYS A 66 . ? 1_555 ? 19 AC8 6 GLN A 72 ? GLN A 71 . ? 1_555 ? 20 AC8 6 SER A 81 ? SER A 80 . ? 1_555 ? 21 AC8 6 TYR A 82 ? TYR A 81 . ? 1_555 ? # _atom_sites.entry_id 3RH2 _atom_sites.fract_transf_matrix[1][1] 0.008095 _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] 0.008095 _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] 0.020181 _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 N O P S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 LYS 3 2 2 LYS LYS A . n A 1 4 THR 4 3 3 THR THR A . n A 1 5 ARG 5 4 4 ARG ARG A . n A 1 6 ASP 6 5 5 ASP ASP A . n A 1 7 LYS 7 6 6 LYS LYS A . n A 1 8 ILE 8 7 7 ILE ILE A . n A 1 9 ILE 9 8 8 ILE ILE A . n A 1 10 GLN 10 9 9 GLN GLN A . n A 1 11 ALA 11 10 10 ALA ALA A . n A 1 12 SER 12 11 11 SER SER A . n A 1 13 LEU 13 12 12 LEU LEU A . n A 1 14 GLU 14 13 13 GLU GLU A . n A 1 15 LEU 15 14 14 LEU LEU A . n A 1 16 PHE 16 15 15 PHE PHE A . n A 1 17 ASN 17 16 16 ASN ASN A . n A 1 18 GLU 18 17 17 GLU GLU A . n A 1 19 HIS 19 18 18 HIS HIS A . n A 1 20 GLY 20 19 19 GLY GLY A . n A 1 21 GLU 21 20 20 GLU GLU A . n A 1 22 ARG 22 21 21 ARG ARG A . n A 1 23 THR 23 22 22 THR THR A . n A 1 24 ILE 24 23 23 ILE ILE A . n A 1 25 THR 25 24 24 THR THR A . n A 1 26 THR 26 25 25 THR THR A . n A 1 27 ASN 27 26 26 ASN ASN A . n A 1 28 HIS 28 27 27 HIS HIS A . n A 1 29 ILE 29 28 28 ILE ILE A . n A 1 30 ALA 30 29 29 ALA ALA A . n A 1 31 ALA 31 30 30 ALA ALA A . n A 1 32 HIS 32 31 31 HIS HIS A . n A 1 33 LEU 33 32 32 LEU LEU A . n A 1 34 ASP 34 33 33 ASP ASP A . n A 1 35 ILE 35 34 34 ILE ILE A . n A 1 36 SER 36 35 35 SER SER A . n A 1 37 PRO 37 36 36 PRO PRO A . n A 1 38 GLY 38 37 37 GLY GLY A . n A 1 39 ASN 39 38 38 ASN ASN A . n A 1 40 LEU 40 39 39 LEU LEU A . n A 1 41 TYR 41 40 40 TYR TYR A . n A 1 42 TYR 42 41 41 TYR TYR A . n A 1 43 HIS 43 42 42 HIS HIS A . n A 1 44 PHE 44 43 43 PHE PHE A . n A 1 45 ARG 45 44 44 ARG ARG A . n A 1 46 ASN 46 45 45 ASN ASN A . n A 1 47 LYS 47 46 46 LYS LYS A . n A 1 48 GLU 48 47 47 GLU GLU A . n A 1 49 ASP 49 48 48 ASP ASP A . n A 1 50 ILE 50 49 49 ILE ILE A . n A 1 51 ILE 51 50 50 ILE ILE A . n A 1 52 ARG 52 51 51 ARG ARG A . n A 1 53 CYS 53 52 52 CYS CYS A . n A 1 54 ILE 54 53 53 ILE ILE A . n A 1 55 PHE 55 54 54 PHE PHE A . n A 1 56 ASP 56 55 55 ASP ASP A . n A 1 57 GLN 57 56 56 GLN GLN A . n A 1 58 TYR 58 57 57 TYR TYR A . n A 1 59 GLU 59 58 58 GLU GLU A . n A 1 60 GLN 60 59 59 GLN GLN A . n A 1 61 HIS 61 60 60 HIS HIS A . n A 1 62 LEU 62 61 61 LEU LEU A . n A 1 63 LEU 63 62 62 LEU LEU A . n A 1 64 LEU 64 63 63 LEU LEU A . n A 1 65 GLY 65 64 64 GLY GLY A . n A 1 66 PHE 66 65 65 PHE PHE A . n A 1 67 LYS 67 66 66 LYS LYS A . n A 1 68 PRO 68 67 67 PRO PRO A . n A 1 69 TYR 69 68 68 TYR TYR A . n A 1 70 ALA 70 69 69 ALA ALA A . n A 1 71 ASP 71 70 70 ASP ASP A . n A 1 72 GLN 72 71 71 GLN GLN A . n A 1 73 LYS 73 72 72 LYS LYS A . n A 1 74 VAL 74 73 73 VAL VAL A . n A 1 75 ASP 75 74 74 ASP ASP A . n A 1 76 LEU 76 75 75 LEU LEU A . n A 1 77 GLU 77 76 76 GLU GLU A . n A 1 78 LEU 78 77 77 LEU LEU A . n A 1 79 LEU 79 78 78 LEU LEU A . n A 1 80 MSE 80 79 79 MSE MSE A . n A 1 81 SER 81 80 80 SER SER A . n A 1 82 TYR 82 81 81 TYR TYR A . n A 1 83 PHE 83 82 82 PHE PHE A . n A 1 84 ASP 84 83 83 ASP ASP A . n A 1 85 ALA 85 84 84 ALA ALA A . n A 1 86 MSE 86 85 85 MSE MSE A . n A 1 87 PHE 87 86 86 PHE PHE A . n A 1 88 TYR 88 87 87 TYR TYR A . n A 1 89 THR 89 88 88 THR THR A . n A 1 90 MSE 90 89 89 MSE MSE A . n A 1 91 TRP 91 90 90 TRP TRP A . n A 1 92 GLN 92 91 91 GLN GLN A . n A 1 93 PHE 93 92 92 PHE PHE A . n A 1 94 ARG 94 93 93 ARG ARG A . n A 1 95 PHE 95 94 94 PHE PHE A . n A 1 96 MSE 96 95 95 MSE MSE A . n A 1 97 TYR 97 96 96 TYR TYR A . n A 1 98 ALA 98 97 97 ALA ALA A . n A 1 99 ASN 99 98 98 ASN ASN A . n A 1 100 LEU 100 99 99 LEU LEU A . n A 1 101 ALA 101 100 100 ALA ALA A . n A 1 102 ASP 102 101 101 ASP ASP A . n A 1 103 ILE 103 102 102 ILE ILE A . n A 1 104 LEU 104 103 103 LEU LEU A . n A 1 105 ALA 105 104 104 ALA ALA A . n A 1 106 ARG 106 105 105 ARG ARG A . n A 1 107 ASP 107 106 106 ASP ASP A . n A 1 108 ASP 108 107 107 ASP ASP A . n A 1 109 THR 109 108 108 THR THR A . n A 1 110 LEU 110 109 109 LEU LEU A . n A 1 111 LYS 111 110 110 LYS LYS A . n A 1 112 ALA 112 111 111 ALA ALA A . n A 1 113 ARG 113 112 112 ARG ARG A . n A 1 114 TYR 114 113 113 TYR TYR A . n A 1 115 LEU 115 114 114 LEU LEU A . n A 1 116 LYS 116 115 115 LYS LYS A . n A 1 117 VAL 117 116 116 VAL VAL A . n A 1 118 GLN 118 117 117 GLN GLN A . n A 1 119 GLN 119 118 118 GLN GLN A . n A 1 120 ALA 120 119 119 ALA ALA A . n A 1 121 VAL 121 120 120 VAL VAL A . n A 1 122 LEU 122 121 121 LEU LEU A . n A 1 123 GLU 123 122 122 GLU GLU A . n A 1 124 GLN 124 123 123 GLN GLN A . n A 1 125 SER 125 124 124 SER SER A . n A 1 126 ILE 126 125 125 ILE ILE A . n A 1 127 ALA 127 126 126 ALA ALA A . n A 1 128 VAL 128 127 127 VAL VAL A . n A 1 129 LEU 129 128 128 LEU LEU A . n A 1 130 ASN 130 129 129 ASN ASN A . n A 1 131 GLN 131 130 130 GLN GLN A . n A 1 132 LEU 132 131 131 LEU LEU A . n A 1 133 LYS 133 132 132 LYS LYS A . n A 1 134 LYS 134 133 133 LYS LYS A . n A 1 135 ASP 135 134 134 ASP ASP A . n A 1 136 GLY 136 135 135 GLY GLY A . n A 1 137 ILE 137 136 136 ILE ILE A . n A 1 138 LEU 138 137 137 LEU LEU A . n A 1 139 GLN 139 138 138 GLN GLN A . n A 1 140 ILE 140 139 139 ILE ILE A . n A 1 141 GLU 141 140 140 GLU GLU A . n A 1 142 ASP 142 141 141 ASP ASP A . n A 1 143 GLU 143 142 142 GLU GLU A . n A 1 144 ARG 144 143 143 ARG ARG A . n A 1 145 ILE 145 144 144 ILE ILE A . n A 1 146 ALA 146 145 145 ALA ALA A . n A 1 147 ASP 147 146 146 ASP ASP A . n A 1 148 LEU 148 147 147 LEU LEU A . n A 1 149 ALA 149 148 148 ALA ALA A . n A 1 150 ASP 150 149 149 ASP ASP A . n A 1 151 THR 151 150 150 THR THR A . n A 1 152 ILE 152 151 151 ILE ILE A . n A 1 153 LYS 153 152 152 LYS LYS A . n A 1 154 MSE 154 153 153 MSE MSE A . n A 1 155 ILE 155 154 154 ILE ILE A . n A 1 156 ILE 156 155 155 ILE ILE A . n A 1 157 GLY 157 156 156 GLY GLY A . n A 1 158 PHE 158 157 157 PHE PHE A . n A 1 159 TRP 159 158 158 TRP TRP A . n A 1 160 ILE 160 159 159 ILE ILE A . n A 1 161 SER 161 160 160 SER SER A . n A 1 162 TYR 162 161 161 TYR TYR A . n A 1 163 LYS 163 162 162 LYS LYS A . n A 1 164 LEU 164 163 163 LEU LEU A . n A 1 165 THR 165 164 164 THR THR A . n A 1 166 GLN 166 165 165 GLN GLN A . n A 1 167 SER 167 166 166 SER SER A . n A 1 168 SER 168 167 167 SER SER A . n A 1 169 ILE 169 168 168 ILE ILE A . n A 1 170 ALA 170 169 169 ALA ALA A . n A 1 171 THR 171 170 170 THR THR A . n A 1 172 ILE 172 171 171 ILE ILE A . n A 1 173 SER 173 172 172 SER SER A . n A 1 174 LYS 174 173 173 LYS LYS A . n A 1 175 ALA 175 174 174 ALA ALA A . n A 1 176 SER 176 175 175 SER SER A . n A 1 177 LEU 177 176 176 LEU LEU A . n A 1 178 TYR 178 177 177 TYR TYR A . n A 1 179 GLU 179 178 178 GLU GLU A . n A 1 180 GLY 180 179 179 GLY GLY A . n A 1 181 LEU 181 180 180 LEU LEU A . n A 1 182 LEU 182 181 181 LEU LEU A . n A 1 183 ARG 183 182 182 ARG ARG A . n A 1 184 VAL 184 183 183 VAL VAL A . n A 1 185 LEU 185 184 184 LEU LEU A . n A 1 186 MSE 186 185 185 MSE MSE A . n A 1 187 ILE 187 186 186 ILE ILE A . n A 1 188 PHE 188 187 187 PHE PHE A . n A 1 189 LYS 189 188 188 LYS LYS A . n A 1 190 ALA 190 189 189 ALA ALA A . n A 1 191 TYR 191 190 190 TYR TYR A . n A 1 192 SER 192 191 191 SER SER A . n A 1 193 THR 193 192 192 THR THR A . n A 1 194 PRO 194 193 193 PRO PRO A . n A 1 195 ASP 195 194 194 ASP ASP A . n A 1 196 SER 196 195 195 SER SER A . n A 1 197 LEU 197 196 196 LEU LEU A . n A 1 198 ALA 198 197 197 ALA ALA A . n A 1 199 ASN 199 198 198 ASN ASN A . n A 1 200 PHE 200 199 199 PHE PHE A . n A 1 201 ASP 201 200 200 ASP ASP A . n A 1 202 ARG 202 201 201 ARG ARG A . n A 1 203 LEU 203 202 202 LEU LEU A . n A 1 204 GLU 204 203 203 GLU GLU A . n A 1 205 GLN 205 204 204 GLN GLN A . n A 1 206 HIS 206 205 205 HIS HIS A . n A 1 207 PHE 207 206 206 PHE PHE A . n A 1 208 ARG 208 207 207 ARG ARG A . n A 1 209 SER 209 208 208 SER SER A . n A 1 210 GLN 210 209 209 GLN GLN A . n A 1 211 SER 211 210 210 SER SER A . n A 1 212 ASN 212 211 ? ? ? A . n # _pdbx_SG_project.project_name PSI:Biology _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 UNL 1 301 301 UNL UNL A . C 3 PO4 1 302 302 PO4 PO4 A . D 3 PO4 1 303 303 PO4 PO4 A . E 4 GOL 1 304 304 GOL GOL A . F 4 GOL 1 305 305 GOL GOL A . G 4 GOL 1 306 306 GOL GOL A . H 4 GOL 1 307 307 GOL GOL A . I 4 GOL 1 308 308 GOL GOL A . J 4 GOL 1 309 309 GOL GOL A . K 5 HOH 1 310 310 HOH HOH A . K 5 HOH 2 311 311 HOH HOH A . K 5 HOH 3 312 312 HOH HOH A . K 5 HOH 4 313 313 HOH HOH A . K 5 HOH 5 314 314 HOH HOH A . K 5 HOH 6 315 315 HOH HOH A . K 5 HOH 7 316 316 HOH HOH A . K 5 HOH 8 317 317 HOH HOH A . K 5 HOH 9 318 318 HOH HOH A . K 5 HOH 10 319 319 HOH HOH A . K 5 HOH 11 320 320 HOH HOH A . K 5 HOH 12 321 321 HOH HOH A . K 5 HOH 13 322 322 HOH HOH A . K 5 HOH 14 323 323 HOH HOH A . K 5 HOH 15 324 324 HOH HOH A . K 5 HOH 16 325 325 HOH HOH A . K 5 HOH 17 326 326 HOH HOH A . K 5 HOH 18 327 327 HOH HOH A . K 5 HOH 19 328 328 HOH HOH A . K 5 HOH 20 329 329 HOH HOH A . K 5 HOH 21 330 330 HOH HOH A . K 5 HOH 22 331 331 HOH HOH A . K 5 HOH 23 332 332 HOH HOH A . K 5 HOH 24 333 333 HOH HOH A . K 5 HOH 25 334 334 HOH HOH A . K 5 HOH 26 335 335 HOH HOH A . K 5 HOH 27 336 336 HOH HOH A . K 5 HOH 28 337 337 HOH HOH A . K 5 HOH 29 338 338 HOH HOH A . K 5 HOH 30 339 339 HOH HOH A . K 5 HOH 31 340 340 HOH HOH A . K 5 HOH 32 341 341 HOH HOH A . K 5 HOH 33 342 342 HOH HOH A . K 5 HOH 34 343 343 HOH HOH A . K 5 HOH 35 344 344 HOH HOH A . K 5 HOH 36 345 345 HOH HOH A . K 5 HOH 37 346 346 HOH HOH A . K 5 HOH 38 347 347 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 80 A MSE 79 ? MET SELENOMETHIONINE 3 A MSE 86 A MSE 85 ? MET SELENOMETHIONINE 4 A MSE 90 A MSE 89 ? MET SELENOMETHIONINE 5 A MSE 96 A MSE 95 ? MET SELENOMETHIONINE 6 A MSE 154 A MSE 153 ? MET SELENOMETHIONINE 7 A MSE 186 A MSE 185 ? 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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # 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)' 6600 ? 1 MORE -41 ? 1 'SSA (A^2)' 20170 ? # 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' 7_556 y,x,-z+1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 49.5520000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-05-04 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2014-12-24 4 'Structure model' 1 3 2017-11-08 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' 'Version format compliance' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Database references' 5 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.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 41.5402 _pdbx_refine_tls.origin_y 29.9371 _pdbx_refine_tls.origin_z 13.8352 _pdbx_refine_tls.T[1][1] 0.2031 _pdbx_refine_tls.T[2][2] 0.1792 _pdbx_refine_tls.T[3][3] 0.1134 _pdbx_refine_tls.T[1][2] 0.0293 _pdbx_refine_tls.T[1][3] 0.0345 _pdbx_refine_tls.T[2][3] 0.1185 _pdbx_refine_tls.L[1][1] 3.4092 _pdbx_refine_tls.L[2][2] 2.4395 _pdbx_refine_tls.L[3][3] 1.0418 _pdbx_refine_tls.L[1][2] 0.1508 _pdbx_refine_tls.L[1][3] 0.9434 _pdbx_refine_tls.L[2][3] 0.6798 _pdbx_refine_tls.S[1][1] 0.1025 _pdbx_refine_tls.S[2][2] -0.1131 _pdbx_refine_tls.S[3][3] 0.0106 _pdbx_refine_tls.S[1][2] 0.1588 _pdbx_refine_tls.S[1][3] 0.0506 _pdbx_refine_tls.S[2][3] -0.2833 _pdbx_refine_tls.S[2][1] -0.2524 _pdbx_refine_tls.S[3][1] -0.0319 _pdbx_refine_tls.S[3][2] 0.0036 # _pdbx_refine_tls_group.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 1 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 210 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # _phasing.method MAD # 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 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE 'December 6, 2010' ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 REFMAC 5.5.0110 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 3RH2 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS 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. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ALA _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 69 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -86.10 _pdbx_validate_torsion.psi -109.16 # 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 2 ? CE ? A LYS 3 CE 2 1 Y 1 A LYS 2 ? NZ ? A LYS 3 NZ 3 1 Y 1 A LYS 115 ? CE ? A LYS 116 CE 4 1 Y 1 A LYS 115 ? NZ ? A LYS 116 NZ 5 1 Y 1 A ILE 168 ? CG1 ? A ILE 169 CG1 6 1 Y 1 A ILE 168 ? CG2 ? A ILE 169 CG2 7 1 Y 1 A ILE 168 ? CD1 ? A ILE 169 CD1 8 1 Y 1 A LYS 188 ? CE ? A LYS 189 CE 9 1 Y 1 A LYS 188 ? NZ ? A LYS 189 NZ 10 1 Y 1 A GLN 204 ? CD ? A GLN 205 CD 11 1 Y 1 A GLN 204 ? OE1 ? A GLN 205 OE1 12 1 Y 1 A GLN 204 ? NE2 ? A GLN 205 NE2 13 1 Y 1 A SER 210 ? OG ? A SER 211 OG # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A ASN 211 ? A ASN 212 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'UNKNOWN LIGAND' UNL 3 'PHOSPHATE ION' PO4 4 GLYCEROL GOL 5 water HOH #