data_2PIM # _entry.id 2PIM # _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 2PIM pdb_00002pim 10.2210/pdb2pim/pdb RCSB RCSB042413 ? ? WWPDB D_1000042413 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 370429 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2PIM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-04-13 _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 Phenylacetic acid degradation-related protein (YP_298971.1) from Ralstonia eutropha JMP134 at 2.20 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 2PIM _cell.length_a 111.774 _cell.length_b 111.774 _cell.length_c 46.461 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _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 2PIM _symmetry.Int_Tables_number 177 _symmetry.space_group_name_H-M 'P 6 2 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 'Phenylacetic acid degradation-related protein' 14996.161 1 ? ? ? ? 2 water nat water 18.015 55 ? ? ? ? # _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)SQDNYFSR(MSE)LRGEAPVPAVAGTLGGVIRAVDLEAGSLESDYVATDAFLNPVGQVQGG(MSE)LGA(MSE) LDDVTA(MSE)LVTATLEDGASCSTLNLNLSFLRPAQAGLLRGRARLERRGRNVCNVVGELSQDGKLVATATATC(MSE) VARRA ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSQDNYFSRMLRGEAPVPAVAGTLGGVIRAVDLEAGSLESDYVATDAFLNPVGQVQGGMLGAMLDDVTAMLVTATLEDG ASCSTLNLNLSFLRPAQAGLLRGRARLERRGRNVCNVVGELSQDGKLVATATATCMVARRA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 370429 # 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 GLN n 1 5 ASP n 1 6 ASN n 1 7 TYR n 1 8 PHE n 1 9 SER n 1 10 ARG n 1 11 MSE n 1 12 LEU n 1 13 ARG n 1 14 GLY n 1 15 GLU n 1 16 ALA n 1 17 PRO n 1 18 VAL n 1 19 PRO n 1 20 ALA n 1 21 VAL n 1 22 ALA n 1 23 GLY n 1 24 THR n 1 25 LEU n 1 26 GLY n 1 27 GLY n 1 28 VAL n 1 29 ILE n 1 30 ARG n 1 31 ALA n 1 32 VAL n 1 33 ASP n 1 34 LEU n 1 35 GLU n 1 36 ALA n 1 37 GLY n 1 38 SER n 1 39 LEU n 1 40 GLU n 1 41 SER n 1 42 ASP n 1 43 TYR n 1 44 VAL n 1 45 ALA n 1 46 THR n 1 47 ASP n 1 48 ALA n 1 49 PHE n 1 50 LEU n 1 51 ASN n 1 52 PRO n 1 53 VAL n 1 54 GLY n 1 55 GLN n 1 56 VAL n 1 57 GLN n 1 58 GLY n 1 59 GLY n 1 60 MSE n 1 61 LEU n 1 62 GLY n 1 63 ALA n 1 64 MSE n 1 65 LEU n 1 66 ASP n 1 67 ASP n 1 68 VAL n 1 69 THR n 1 70 ALA n 1 71 MSE n 1 72 LEU n 1 73 VAL n 1 74 THR n 1 75 ALA n 1 76 THR n 1 77 LEU n 1 78 GLU n 1 79 ASP n 1 80 GLY n 1 81 ALA n 1 82 SER n 1 83 CYS n 1 84 SER n 1 85 THR n 1 86 LEU n 1 87 ASN n 1 88 LEU n 1 89 ASN n 1 90 LEU n 1 91 SER n 1 92 PHE n 1 93 LEU n 1 94 ARG n 1 95 PRO n 1 96 ALA n 1 97 GLN n 1 98 ALA n 1 99 GLY n 1 100 LEU n 1 101 LEU n 1 102 ARG n 1 103 GLY n 1 104 ARG n 1 105 ALA n 1 106 ARG n 1 107 LEU n 1 108 GLU n 1 109 ARG n 1 110 ARG n 1 111 GLY n 1 112 ARG n 1 113 ASN n 1 114 VAL n 1 115 CYS n 1 116 ASN n 1 117 VAL n 1 118 VAL n 1 119 GLY n 1 120 GLU n 1 121 LEU n 1 122 SER n 1 123 GLN n 1 124 ASP n 1 125 GLY n 1 126 LYS n 1 127 LEU n 1 128 VAL n 1 129 ALA n 1 130 THR n 1 131 ALA n 1 132 THR n 1 133 ALA n 1 134 THR n 1 135 CYS n 1 136 MSE n 1 137 VAL n 1 138 ALA n 1 139 ARG n 1 140 ARG n 1 141 ALA 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 Cupriavidus _entity_src_gen.pdbx_gene_src_gene 'YP_298971.1, Reut_B4779' _entity_src_gen.gene_src_species 'Cupriavidus necator' _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 'Ralstonia eutropha JMP134' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 264198 _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 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 Q46RV7_RALEJ _struct_ref.pdbx_db_accession Q46RV7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSQDNYFSRMLRGEAPVPAVAGTLGGVIRAVDLEAGSLESDYVATDAFLNPVGQVQGGMLGAMLDDVTAMLVTATLEDGA SCSTLNLNLSFLRPAQAGLLRGRARLERRGRNVCNVVGELSQDGKLVATATATCMVARRA ; _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 2PIM _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 141 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q46RV7 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 140 _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 140 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2PIM _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 Q46RV7 _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 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 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 2PIM # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.79 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 55.96 _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 6.86 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details 'NANODROP, 1.32M Sodium citrate, 0.1M Sodium cacodylate pH 6.86, 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 0.91837 1.0 2 0.97934 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' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 2PIM _reflns.d_resolution_high 2.20 _reflns.d_resolution_low 28.748 _reflns.number_obs 9118 _reflns.pdbx_Rmerge_I_obs 0.141 _reflns.pdbx_netI_over_sigmaI 4.700 _reflns.pdbx_Rsym_value 0.141 _reflns.pdbx_redundancy 14.100 _reflns.percent_possible_obs 100.000 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_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 2.20 2.26 ? 9251 ? 0.894 0.8 0.894 ? 14.30 ? 646 100.00 1 1 2.26 2.32 ? 9332 ? 0.777 1.0 0.777 ? 14.50 ? 644 100.00 2 1 2.32 2.39 ? 8976 ? 0.673 1.1 0.673 ? 14.50 ? 621 100.00 3 1 2.39 2.46 ? 8844 ? 0.657 1.1 0.657 ? 14.40 ? 614 100.00 4 1 2.46 2.54 ? 8384 ? 0.490 1.5 0.490 ? 14.50 ? 578 100.00 5 1 2.54 2.63 ? 8254 ? 0.424 1.8 0.424 ? 14.40 ? 574 100.00 6 1 2.63 2.73 ? 7872 ? 0.359 2.1 0.359 ? 14.40 ? 547 100.00 7 1 2.73 2.84 ? 7580 ? 0.310 2.5 0.310 ? 14.40 ? 528 100.00 8 1 2.84 2.97 ? 7417 ? 0.225 3.3 0.225 ? 14.30 ? 520 100.00 9 1 2.97 3.11 ? 7058 ? 0.178 4.2 0.178 ? 14.20 ? 496 100.00 10 1 3.11 3.28 ? 6607 ? 0.137 5.3 0.137 ? 14.20 ? 465 100.00 11 1 3.28 3.48 ? 6180 ? 0.115 5.8 0.115 ? 14.00 ? 443 100.00 12 1 3.48 3.72 ? 5901 ? 0.098 6.9 0.098 ? 14.00 ? 423 100.00 13 1 3.72 4.02 ? 5468 ? 0.082 8.1 0.082 ? 13.80 ? 397 100.00 14 1 4.02 4.40 ? 5098 ? 0.070 9.3 0.070 ? 13.80 ? 370 100.00 15 1 4.40 4.92 ? 4570 ? 0.061 10.7 0.061 ? 13.60 ? 336 100.00 16 1 4.92 5.68 ? 4076 ? 0.078 8.3 0.078 ? 13.40 ? 305 100.00 17 1 5.68 6.96 ? 3411 ? 0.079 8.2 0.079 ? 13.00 ? 263 100.00 18 1 6.96 9.84 ? 2640 ? 0.052 10.3 0.052 ? 12.20 ? 216 100.00 19 1 9.84 28.75 ? 1349 ? 0.058 10.0 0.058 ? 10.20 ? 132 96.60 20 1 # _refine.entry_id 2PIM _refine.ls_d_res_high 2.200 _refine.ls_d_res_low 28.748 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 100.000 _refine.ls_number_reflns_obs 9116 _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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. ; _refine.ls_R_factor_all 0.185 _refine.ls_R_factor_R_work 0.182 _refine.ls_R_factor_R_free 0.222 _refine.ls_percent_reflns_R_free 5.600 _refine.ls_number_reflns_R_free 514 _refine.B_iso_mean 28.728 _refine.aniso_B[1][1] -2.320 _refine.aniso_B[2][2] -2.320 _refine.aniso_B[3][3] 3.490 _refine.aniso_B[1][2] -1.160 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.950 _refine.pdbx_overall_ESU_R 0.196 _refine.pdbx_overall_ESU_R_Free 0.172 _refine.overall_SU_ML 0.139 _refine.overall_SU_B 11.181 _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 0.185 _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_overall_phase_error ? _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 956 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 55 _refine_hist.number_atoms_total 1011 _refine_hist.d_res_high 2.200 _refine_hist.d_res_low 28.748 # 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 986 0.016 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 948 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1338 1.604 1.984 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2180 0.803 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 135 6.366 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 40 40.336 23.250 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 163 16.046 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 11 12.453 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 161 0.094 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1137 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 198 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 171 0.194 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 921 0.186 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 477 0.167 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 670 0.088 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 42 0.201 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 14 0.229 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 66 0.281 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 5 0.165 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 773 2.173 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 281 0.518 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1049 2.990 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 345 5.773 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 289 7.143 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.200 _refine_ls_shell.d_res_low 2.257 _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 616 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.220 _refine_ls_shell.R_factor_R_free 0.296 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 643 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2PIM _struct.title ;CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE, PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN (REUT_B4779) FROM RALSTONIA EUTROPHA JMP134 AT 2.20 A RESOLUTION ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;THIOESTERASE SUPERFAMILY, PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE ; _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.entry_id 2PIM # 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 ? # _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 ASN A 6 ? ARG A 13 ? ASN A 5 ARG A 12 1 ? 8 HELX_P HELX_P2 2 PRO A 19 ? GLY A 26 ? PRO A 18 GLY A 25 1 ? 8 HELX_P HELX_P3 3 THR A 46 ? LEU A 50 ? THR A 45 LEU A 49 5 ? 5 HELX_P HELX_P4 4 GLN A 57 ? THR A 76 ? GLN A 56 THR A 75 1 ? 20 # _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 ARG 10 C ? ? ? 1_555 A MSE 11 N ? ? A ARG 9 A MSE 10 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale2 covale both ? A MSE 11 C ? ? ? 1_555 A LEU 12 N ? ? A MSE 10 A LEU 11 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale3 covale both ? A GLY 59 C ? ? ? 1_555 A MSE 60 N ? ? A GLY 58 A MSE 59 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale4 covale both ? A MSE 60 C ? ? ? 1_555 A LEU 61 N ? ? A MSE 59 A LEU 60 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale5 covale both ? A ALA 63 C ? ? ? 1_555 A MSE 64 N ? ? A ALA 62 A MSE 63 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale6 covale both ? A MSE 64 C ? ? ? 1_555 A LEU 65 N ? ? A MSE 63 A LEU 64 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale7 covale both ? A ALA 70 C ? ? ? 1_555 A MSE 71 N ? ? A ALA 69 A MSE 70 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale8 covale both ? A MSE 71 C ? ? ? 1_555 A LEU 72 N ? ? A MSE 70 A LEU 71 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale9 covale both ? A CYS 135 C ? ? ? 1_555 A MSE 136 N ? ? A CYS 134 A MSE 135 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale10 covale both ? A MSE 136 C ? ? ? 1_555 A VAL 137 N ? ? A MSE 135 A VAL 136 1_555 ? ? ? ? ? ? ? 1.338 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _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 # 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 VAL A 28 ? ASP A 33 ? VAL A 27 ASP A 32 A 2 SER A 38 ? ALA A 45 ? SER A 37 ALA A 44 A 3 GLY A 99 ? ARG A 110 ? GLY A 98 ARG A 109 A 4 VAL A 114 ? GLN A 123 ? VAL A 113 GLN A 122 A 5 LYS A 126 ? MSE A 136 ? LYS A 125 MSE A 135 A 6 SER A 84 ? PHE A 92 ? SER A 83 PHE A 91 # 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 VAL A 28 ? N VAL A 27 O ASP A 42 ? O ASP A 41 A 2 3 N SER A 41 ? N SER A 40 O GLY A 103 ? O GLY A 102 A 3 4 N ARG A 106 ? N ARG A 105 O VAL A 118 ? O VAL A 117 A 4 5 N LEU A 121 ? N LEU A 120 O VAL A 128 ? O VAL A 127 A 5 6 O MSE A 136 ? O MSE A 135 N SER A 84 ? N SER A 83 # _atom_sites.entry_id 2PIM _atom_sites.fract_transf_matrix[1][1] 0.00895 _atom_sites.fract_transf_matrix[1][2] 0.00516 _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] 0.01033 _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] 0.02152 _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 ? ? ? A . n A 1 2 MSE 2 1 ? ? ? A . n A 1 3 SER 3 2 ? ? ? A . n A 1 4 GLN 4 3 ? ? ? A . n A 1 5 ASP 5 4 ? ? ? A . n A 1 6 ASN 6 5 5 ASN ASN A . n A 1 7 TYR 7 6 6 TYR TYR A . n A 1 8 PHE 8 7 7 PHE PHE A . n A 1 9 SER 9 8 8 SER SER A . n A 1 10 ARG 10 9 9 ARG ARG A . n A 1 11 MSE 11 10 10 MSE MSE A . n A 1 12 LEU 12 11 11 LEU LEU A . n A 1 13 ARG 13 12 12 ARG ARG A . n A 1 14 GLY 14 13 13 GLY GLY A . n A 1 15 GLU 15 14 14 GLU GLU A . n A 1 16 ALA 16 15 15 ALA ALA A . n A 1 17 PRO 17 16 16 PRO PRO A . n A 1 18 VAL 18 17 17 VAL VAL A . n A 1 19 PRO 19 18 18 PRO PRO A . n A 1 20 ALA 20 19 19 ALA ALA A . n A 1 21 VAL 21 20 20 VAL VAL A . n A 1 22 ALA 22 21 21 ALA ALA A . n A 1 23 GLY 23 22 22 GLY GLY A . n A 1 24 THR 24 23 23 THR THR A . n A 1 25 LEU 25 24 24 LEU LEU A . n A 1 26 GLY 26 25 25 GLY GLY A . n A 1 27 GLY 27 26 26 GLY GLY A . n A 1 28 VAL 28 27 27 VAL VAL A . n A 1 29 ILE 29 28 28 ILE ILE A . n A 1 30 ARG 30 29 29 ARG ARG A . n A 1 31 ALA 31 30 30 ALA ALA A . n A 1 32 VAL 32 31 31 VAL VAL A . n A 1 33 ASP 33 32 32 ASP ASP A . n A 1 34 LEU 34 33 33 LEU LEU A . n A 1 35 GLU 35 34 34 GLU GLU A . n A 1 36 ALA 36 35 35 ALA ALA A . n A 1 37 GLY 37 36 36 GLY GLY A . n A 1 38 SER 38 37 37 SER SER A . n A 1 39 LEU 39 38 38 LEU LEU A . n A 1 40 GLU 40 39 39 GLU GLU A . n A 1 41 SER 41 40 40 SER SER A . n A 1 42 ASP 42 41 41 ASP ASP A . n A 1 43 TYR 43 42 42 TYR TYR A . n A 1 44 VAL 44 43 43 VAL VAL A . n A 1 45 ALA 45 44 44 ALA ALA A . n A 1 46 THR 46 45 45 THR THR A . n A 1 47 ASP 47 46 46 ASP ASP A . n A 1 48 ALA 48 47 47 ALA ALA A . n A 1 49 PHE 49 48 48 PHE PHE A . n A 1 50 LEU 50 49 49 LEU LEU A . n A 1 51 ASN 51 50 50 ASN ASN A . n A 1 52 PRO 52 51 51 PRO PRO A . n A 1 53 VAL 53 52 52 VAL VAL A . n A 1 54 GLY 54 53 53 GLY GLY A . n A 1 55 GLN 55 54 54 GLN GLN A . n A 1 56 VAL 56 55 55 VAL VAL A . n A 1 57 GLN 57 56 56 GLN GLN A . n A 1 58 GLY 58 57 57 GLY GLY A . n A 1 59 GLY 59 58 58 GLY GLY A . n A 1 60 MSE 60 59 59 MSE MSE A . n A 1 61 LEU 61 60 60 LEU LEU A . n A 1 62 GLY 62 61 61 GLY GLY A . n A 1 63 ALA 63 62 62 ALA ALA A . n A 1 64 MSE 64 63 63 MSE MSE A . n A 1 65 LEU 65 64 64 LEU LEU A . n A 1 66 ASP 66 65 65 ASP ASP A . n A 1 67 ASP 67 66 66 ASP ASP A . n A 1 68 VAL 68 67 67 VAL VAL A . n A 1 69 THR 69 68 68 THR THR A . n A 1 70 ALA 70 69 69 ALA ALA A . n A 1 71 MSE 71 70 70 MSE MSE A . n A 1 72 LEU 72 71 71 LEU LEU A . n A 1 73 VAL 73 72 72 VAL VAL A . n A 1 74 THR 74 73 73 THR THR A . n A 1 75 ALA 75 74 74 ALA ALA A . n A 1 76 THR 76 75 75 THR THR A . n A 1 77 LEU 77 76 76 LEU LEU A . n A 1 78 GLU 78 77 77 GLU GLU A . n A 1 79 ASP 79 78 78 ASP ASP A . n A 1 80 GLY 80 79 79 GLY GLY A . n A 1 81 ALA 81 80 80 ALA ALA A . n A 1 82 SER 82 81 81 SER SER A . n A 1 83 CYS 83 82 82 CYS CYS A . n A 1 84 SER 84 83 83 SER SER A . n A 1 85 THR 85 84 84 THR THR A . n A 1 86 LEU 86 85 85 LEU LEU A . n A 1 87 ASN 87 86 86 ASN ASN A . n A 1 88 LEU 88 87 87 LEU LEU A . n A 1 89 ASN 89 88 88 ASN ASN A . n A 1 90 LEU 90 89 89 LEU LEU A . n A 1 91 SER 91 90 90 SER SER A . n A 1 92 PHE 92 91 91 PHE PHE A . n A 1 93 LEU 93 92 92 LEU LEU A . n A 1 94 ARG 94 93 93 ARG ARG A . n A 1 95 PRO 95 94 94 PRO PRO A . n A 1 96 ALA 96 95 95 ALA ALA A . n A 1 97 GLN 97 96 96 GLN GLN A . n A 1 98 ALA 98 97 97 ALA ALA A . n A 1 99 GLY 99 98 98 GLY GLY A . n A 1 100 LEU 100 99 99 LEU LEU A . n A 1 101 LEU 101 100 100 LEU LEU A . n A 1 102 ARG 102 101 101 ARG ARG A . n A 1 103 GLY 103 102 102 GLY GLY A . n A 1 104 ARG 104 103 103 ARG ARG 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 LEU 107 106 106 LEU LEU A . n A 1 108 GLU 108 107 107 GLU GLU A . n A 1 109 ARG 109 108 108 ARG ARG A . n A 1 110 ARG 110 109 109 ARG ARG A . n A 1 111 GLY 111 110 110 GLY GLY A . n A 1 112 ARG 112 111 111 ARG ARG A . n A 1 113 ASN 113 112 112 ASN ASN A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 CYS 115 114 114 CYS CYS A . n A 1 116 ASN 116 115 115 ASN ASN A . n A 1 117 VAL 117 116 116 VAL VAL A . n A 1 118 VAL 118 117 117 VAL VAL A . n A 1 119 GLY 119 118 118 GLY GLY A . n A 1 120 GLU 120 119 119 GLU GLU A . n A 1 121 LEU 121 120 120 LEU LEU A . n A 1 122 SER 122 121 121 SER SER A . n A 1 123 GLN 123 122 122 GLN GLN A . n A 1 124 ASP 124 123 123 ASP ASP A . n A 1 125 GLY 125 124 124 GLY GLY A . n A 1 126 LYS 126 125 125 LYS LYS A . n A 1 127 LEU 127 126 126 LEU LEU A . n A 1 128 VAL 128 127 127 VAL VAL A . n A 1 129 ALA 129 128 128 ALA ALA A . n A 1 130 THR 130 129 129 THR THR A . n A 1 131 ALA 131 130 130 ALA ALA A . n A 1 132 THR 132 131 131 THR THR A . n A 1 133 ALA 133 132 132 ALA ALA A . n A 1 134 THR 134 133 133 THR THR A . n A 1 135 CYS 135 134 134 CYS CYS A . n A 1 136 MSE 136 135 135 MSE MSE A . n A 1 137 VAL 137 136 136 VAL VAL A . n A 1 138 ALA 138 137 ? ? ? A . n A 1 139 ARG 139 138 ? ? ? A . n A 1 140 ARG 140 139 ? ? ? A . n A 1 141 ALA 141 140 ? ? ? 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 HOH 1 141 1 HOH HOH A . B 2 HOH 2 142 2 HOH HOH A . B 2 HOH 3 143 3 HOH HOH A . B 2 HOH 4 144 4 HOH HOH A . B 2 HOH 5 145 5 HOH HOH A . B 2 HOH 6 146 6 HOH HOH A . B 2 HOH 7 147 7 HOH HOH A . B 2 HOH 8 148 8 HOH HOH A . B 2 HOH 9 149 9 HOH HOH A . B 2 HOH 10 150 10 HOH HOH A . B 2 HOH 11 151 11 HOH HOH A . B 2 HOH 12 152 12 HOH HOH A . B 2 HOH 13 153 13 HOH HOH A . B 2 HOH 14 154 14 HOH HOH A . B 2 HOH 15 155 15 HOH HOH A . B 2 HOH 16 156 16 HOH HOH A . B 2 HOH 17 157 17 HOH HOH A . B 2 HOH 18 158 18 HOH HOH A . B 2 HOH 19 159 19 HOH HOH A . B 2 HOH 20 160 20 HOH HOH A . B 2 HOH 21 161 21 HOH HOH A . B 2 HOH 22 162 22 HOH HOH A . B 2 HOH 23 163 23 HOH HOH A . B 2 HOH 24 164 24 HOH HOH A . B 2 HOH 25 165 25 HOH HOH A . B 2 HOH 26 166 26 HOH HOH A . B 2 HOH 27 167 27 HOH HOH A . B 2 HOH 28 168 28 HOH HOH A . B 2 HOH 29 169 29 HOH HOH A . B 2 HOH 30 170 30 HOH HOH A . B 2 HOH 31 171 31 HOH HOH A . B 2 HOH 32 172 32 HOH HOH A . B 2 HOH 33 173 33 HOH HOH A . B 2 HOH 34 174 34 HOH HOH A . B 2 HOH 35 175 35 HOH HOH A . B 2 HOH 36 176 36 HOH HOH A . B 2 HOH 37 177 37 HOH HOH A . B 2 HOH 38 178 38 HOH HOH A . B 2 HOH 39 179 39 HOH HOH A . B 2 HOH 40 180 40 HOH HOH A . B 2 HOH 41 181 41 HOH HOH A . B 2 HOH 42 182 42 HOH HOH A . B 2 HOH 43 183 43 HOH HOH A . B 2 HOH 44 184 44 HOH HOH A . B 2 HOH 45 185 45 HOH HOH A . B 2 HOH 46 186 46 HOH HOH A . B 2 HOH 47 187 47 HOH HOH A . B 2 HOH 48 188 48 HOH HOH A . B 2 HOH 49 189 49 HOH HOH A . B 2 HOH 50 190 50 HOH HOH A . B 2 HOH 51 191 51 HOH HOH A . B 2 HOH 52 192 52 HOH HOH A . B 2 HOH 53 193 53 HOH HOH A . B 2 HOH 54 194 54 HOH HOH A . B 2 HOH 55 195 55 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 11 A MSE 10 ? MET SELENOMETHIONINE 2 A MSE 60 A MSE 59 ? MET SELENOMETHIONINE 3 A MSE 64 A MSE 63 ? MET SELENOMETHIONINE 4 A MSE 71 A MSE 70 ? MET SELENOMETHIONINE 5 A MSE 136 A MSE 135 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 software_defined_assembly PQS tetrameric 4 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B 2 1,3,2,4 A,B # 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)' 2020 ? 1 MORE -12 ? 1 'SSA (A^2)' 11920 ? # 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_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 3 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 55.8870000000 0.0000000000 -1.0000000000 0.0000000000 96.7991234826 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z 0.5000000000 -0.8660254038 0.0000000000 55.8870000000 -0.8660254038 -0.5000000000 0.0000000000 96.7991234826 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 181 ? B HOH . 2 1 A HOH 189 ? B HOH . # 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 2007-05-01 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' 'Derived calculations' 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 # 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' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.pdbx_refine_id 1 ? refined 30.1710 25.0930 12.7050 -0.0143 0.0346 0.1532 0.0060 -0.1179 0.2541 6.2565 4.4029 1.9723 0.3365 1.3065 0.5073 0.1252 -0.0672 -0.0581 -1.1765 -0.9404 -0.2662 0.7783 0.1610 -0.1173 'X-RAY DIFFRACTION' 2 ? refined 30.0550 34.6070 2.4780 -0.2191 -0.2021 -0.1041 0.0142 -0.0382 0.0721 3.1987 3.8870 1.5203 -0.5162 0.1101 0.0772 0.1095 -0.0454 -0.0641 -0.3252 -0.4832 -0.1479 0.0631 0.0998 0.0494 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _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 _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 6 A 37 ALL A 5 A 36 'X-RAY DIFFRACTION' ? 2 2 A 38 A 137 ALL A 37 A 136 'X-RAY DIFFRACTION' ? # _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 5.2.0005 ? 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 CCP4 '(SCALA)' ? ? ? ? 'data scaling' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? 9 autoSHARP . ? ? ? ? phasing ? ? ? 10 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ; SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. ; # 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 MSE 1 ? A MSE 2 3 1 Y 1 A SER 2 ? A SER 3 4 1 Y 1 A GLN 3 ? A GLN 4 5 1 Y 1 A ASP 4 ? A ASP 5 6 1 Y 1 A ALA 137 ? A ALA 138 7 1 Y 1 A ARG 138 ? A ARG 139 8 1 Y 1 A ARG 139 ? A ARG 140 9 1 Y 1 A ALA 140 ? A ALA 141 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #