data_2YHC # _entry.id 2YHC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YHC PDBE EBI-48152 WWPDB D_1290048152 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2YH9 _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'CRYSTAL STRUCTURE OF THE DIMERIC BAME FROM E. COLI' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YHC _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2011-04-28 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zeth, K.' 1 'Albrecht, R.' 2 # _citation.id primary _citation.title 'Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 286 _citation.page_first 27792 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21586578 _citation.pdbx_database_id_DOI 10.1074/JBC.M111.238931 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Albrecht, R.' 1 primary 'Zeth, K.' 2 # _cell.entry_id 2YHC _cell.length_a 53.112 _cell.length_b 33.428 _cell.length_c 57.783 _cell.angle_alpha 90.00 _cell.angle_beta 111.41 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YHC _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 # 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 'UPF0169 LIPOPROTEIN YFIO' 25959.949 1 ? ? 'RESIDUES 29-245' ? 2 non-polymer syn UREA 60.055 1 ? ? ? ? 3 water nat water 18.015 84 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name BAMD # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;DNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYV MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTER GAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTLEHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;DNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYV MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTER GAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTLEHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASP n 1 2 ASN n 1 3 PRO n 1 4 PRO n 1 5 ASN n 1 6 GLU n 1 7 ILE n 1 8 TYR n 1 9 ALA n 1 10 THR n 1 11 ALA n 1 12 GLN n 1 13 GLN n 1 14 LYS n 1 15 LEU n 1 16 GLN n 1 17 ASP n 1 18 GLY n 1 19 ASN n 1 20 TRP n 1 21 ARG n 1 22 GLN n 1 23 ALA n 1 24 ILE n 1 25 THR n 1 26 GLN n 1 27 LEU n 1 28 GLU n 1 29 ALA n 1 30 LEU n 1 31 ASP n 1 32 ASN n 1 33 ARG n 1 34 TYR n 1 35 PRO n 1 36 PHE n 1 37 GLY n 1 38 PRO n 1 39 TYR n 1 40 SER n 1 41 GLN n 1 42 GLN n 1 43 VAL n 1 44 GLN n 1 45 LEU n 1 46 ASP n 1 47 LEU n 1 48 ILE n 1 49 TYR n 1 50 ALA n 1 51 TYR n 1 52 TYR n 1 53 LYS n 1 54 ASN n 1 55 ALA n 1 56 ASP n 1 57 LEU n 1 58 PRO n 1 59 LEU n 1 60 ALA n 1 61 GLN n 1 62 ALA n 1 63 ALA n 1 64 ILE n 1 65 ASP n 1 66 ARG n 1 67 PHE n 1 68 ILE n 1 69 ARG n 1 70 LEU n 1 71 ASN n 1 72 PRO n 1 73 THR n 1 74 HIS n 1 75 PRO n 1 76 ASN n 1 77 ILE n 1 78 ASP n 1 79 TYR n 1 80 VAL n 1 81 MET n 1 82 TYR n 1 83 MET n 1 84 ARG n 1 85 GLY n 1 86 LEU n 1 87 THR n 1 88 ASN n 1 89 MET n 1 90 ALA n 1 91 LEU n 1 92 ASP n 1 93 ASP n 1 94 SER n 1 95 ALA n 1 96 LEU n 1 97 GLN n 1 98 GLY n 1 99 PHE n 1 100 PHE n 1 101 GLY n 1 102 VAL n 1 103 ASP n 1 104 ARG n 1 105 SER n 1 106 ASP n 1 107 ARG n 1 108 ASP n 1 109 PRO n 1 110 GLN n 1 111 GLN n 1 112 ALA n 1 113 ARG n 1 114 ALA n 1 115 ALA n 1 116 PHE n 1 117 SER n 1 118 ASP n 1 119 PHE n 1 120 SER n 1 121 LYS n 1 122 LEU n 1 123 VAL n 1 124 ARG n 1 125 GLY n 1 126 TYR n 1 127 PRO n 1 128 ASN n 1 129 SER n 1 130 GLN n 1 131 TYR n 1 132 THR n 1 133 THR n 1 134 ASP n 1 135 ALA n 1 136 THR n 1 137 LYS n 1 138 ARG n 1 139 LEU n 1 140 VAL n 1 141 PHE n 1 142 LEU n 1 143 LYS n 1 144 ASP n 1 145 ARG n 1 146 LEU n 1 147 ALA n 1 148 LYS n 1 149 TYR n 1 150 GLU n 1 151 TYR n 1 152 SER n 1 153 VAL n 1 154 ALA n 1 155 GLU n 1 156 TYR n 1 157 TYR n 1 158 THR n 1 159 GLU n 1 160 ARG n 1 161 GLY n 1 162 ALA n 1 163 TRP n 1 164 VAL n 1 165 ALA n 1 166 VAL n 1 167 VAL n 1 168 ASN n 1 169 ARG n 1 170 VAL n 1 171 GLU n 1 172 GLY n 1 173 MET n 1 174 LEU n 1 175 ARG n 1 176 ASP n 1 177 TYR n 1 178 PRO n 1 179 ASP n 1 180 THR n 1 181 GLN n 1 182 ALA n 1 183 THR n 1 184 ARG n 1 185 ASP n 1 186 ALA n 1 187 LEU n 1 188 PRO n 1 189 LEU n 1 190 MET n 1 191 GLU n 1 192 ASN n 1 193 ALA n 1 194 TYR n 1 195 ARG n 1 196 GLN n 1 197 MET n 1 198 GLN n 1 199 MET n 1 200 ASN n 1 201 ALA n 1 202 GLN n 1 203 ALA n 1 204 GLU n 1 205 LYS n 1 206 VAL n 1 207 ALA n 1 208 LYS n 1 209 ILE n 1 210 ILE n 1 211 ALA n 1 212 ALA n 1 213 ASN n 1 214 SER n 1 215 SER n 1 216 ASN n 1 217 THR n 1 218 LEU n 1 219 GLU n 1 220 HIS n 1 221 HIS n 1 222 HIS n 1 223 HIS n 1 224 HIS n 1 225 HIS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 469008 _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 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type 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 PET24D _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code YFIO_ECOLI _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P0AC02 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YHC _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 217 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0AC02 _struct_ref_seq.db_align_beg 29 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 245 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 9 _struct_ref_seq.pdbx_auth_seq_align_end 225 # 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 2YHC LEU A 218 ? UNP P0AC02 ? ? 'expression tag' 226 1 1 2YHC GLU A 219 ? UNP P0AC02 ? ? 'expression tag' 227 2 1 2YHC HIS A 220 ? UNP P0AC02 ? ? 'expression tag' 228 3 1 2YHC HIS A 221 ? UNP P0AC02 ? ? 'expression tag' 229 4 1 2YHC HIS A 222 ? UNP P0AC02 ? ? 'expression tag' 230 5 1 2YHC HIS A 223 ? UNP P0AC02 ? ? 'expression tag' 231 6 1 2YHC HIS A 224 ? UNP P0AC02 ? ? 'expression tag' 232 7 1 2YHC HIS A 225 ? UNP P0AC02 ? ? 'expression tag' 233 8 1 2YHC GLN A 111 ? UNP P0AC02 HIS 139 conflict 119 9 # 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 URE non-polymer . UREA ? 'C H4 N2 O' 60.055 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2YHC _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.84 _exptl_crystal.density_percent_sol 33.14 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '30% PEG 4000, 10% I-PROH, 0.1 M HEPES PH 7.5 .' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X10SA _diffrn_source.pdbx_wavelength 1 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2YHC _reflns.observed_criterion_sigma_I 3.9 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 40.00 _reflns.d_resolution_high 1.80 _reflns.number_obs 16896 _reflns.number_all ? _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.04 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 20.30 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.2 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.90 _reflns_shell.percent_possible_all 97.8 _reflns_shell.Rmerge_I_obs 0.51 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.90 _reflns_shell.pdbx_redundancy ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2YHC _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 16896 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 28.39 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.20007 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19831 _refine.ls_R_factor_R_free 0.23262 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 890 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.959 _refine.correlation_coeff_Fo_to_Fc_free 0.946 _refine.B_iso_mean 44.667 _refine.aniso_B[1][1] 0.53 _refine.aniso_B[2][2] -0.44 _refine.aniso_B[3][3] 0.33 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.58 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct MIRAS _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.157 _refine.pdbx_overall_ESU_R_Free 0.139 _refine.overall_SU_ML 0.100 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 7.041 _refine.overall_SU_R_Cruickshank_DPI ? _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 1704 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 1792 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 28.39 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.024 0.022 ? 1774 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.095 1.936 ? 2415 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.794 5.000 ? 215 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38.216 24.040 ? 99 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 19.081 15.000 ? 289 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.730 15.000 ? 14 'X-RAY DIFFRACTION' ? r_chiral_restr 0.156 0.200 ? 255 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.012 0.021 ? 1405 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.320 1.500 ? 1063 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.317 2.000 ? 1710 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 4.005 3.000 ? 711 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 6.231 4.500 ? 701 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.800 _refine_ls_shell.d_res_low 1.847 _refine_ls_shell.number_reflns_R_work 1234 _refine_ls_shell.R_factor_R_work 0.273 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.371 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 65 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2YHC _struct.title 'Structure of BamD from E. coli' _struct.pdbx_descriptor 'UPF0169 LIPOPROTEIN YFIO' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YHC _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' _struct_keywords.text 'LIPOPROTEIN, ESSENTIAL BAM COMPONENT, MEMBRANE PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 PRO A 3 ? GLY A 18 ? PRO A 11 GLY A 26 1 ? 16 HELX_P HELX_P2 2 ASN A 19 ? TYR A 34 ? ASN A 27 TYR A 42 1 ? 16 HELX_P HELX_P3 3 TYR A 39 ? ASN A 54 ? TYR A 47 ASN A 62 1 ? 16 HELX_P HELX_P4 4 ASP A 56 ? ASN A 71 ? ASP A 64 ASN A 79 1 ? 16 HELX_P HELX_P5 5 ASN A 76 ? ASP A 93 ? ASN A 84 ASP A 101 1 ? 18 HELX_P HELX_P6 6 PRO A 109 ? ARG A 124 ? PRO A 117 ARG A 132 1 ? 16 HELX_P HELX_P7 7 TYR A 131 ? GLY A 161 ? TYR A 139 GLY A 169 1 ? 31 HELX_P HELX_P8 8 ALA A 162 ? TYR A 177 ? ALA A 170 TYR A 185 1 ? 16 HELX_P HELX_P9 9 THR A 180 ? MET A 197 ? THR A 188 MET A 205 1 ? 18 HELX_P HELX_P10 10 MET A 199 ? ASN A 213 ? MET A 207 ASN A 221 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 4 _struct_site.details 'BINDING SITE FOR RESIDUE URE A 1234' # 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 ALA A 165 ? ALA A 173 . ? 1_555 ? 2 AC1 4 ASN A 168 ? ASN A 176 . ? 1_555 ? 3 AC1 4 ARG A 169 ? ARG A 177 . ? 1_555 ? 4 AC1 4 HOH C . ? HOH A 2065 . ? 1_555 ? # _database_PDB_matrix.entry_id 2YHC _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2YHC _atom_sites.fract_transf_matrix[1][1] 0.018828 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007382 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.029915 _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] 0.018589 _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 # 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 ASP 1 9 ? ? ? A . n A 1 2 ASN 2 10 ? ? ? A . n A 1 3 PRO 3 11 11 PRO PRO A . n A 1 4 PRO 4 12 12 PRO PRO A . n A 1 5 ASN 5 13 13 ASN ASN A . n A 1 6 GLU 6 14 14 GLU GLU A . n A 1 7 ILE 7 15 15 ILE ILE A . n A 1 8 TYR 8 16 16 TYR TYR A . n A 1 9 ALA 9 17 17 ALA ALA A . n A 1 10 THR 10 18 18 THR THR A . n A 1 11 ALA 11 19 19 ALA ALA A . n A 1 12 GLN 12 20 20 GLN GLN A . n A 1 13 GLN 13 21 21 GLN GLN A . n A 1 14 LYS 14 22 22 LYS LYS A . n A 1 15 LEU 15 23 23 LEU LEU A . n A 1 16 GLN 16 24 24 GLN GLN A . n A 1 17 ASP 17 25 25 ASP ASP A . n A 1 18 GLY 18 26 26 GLY GLY A . n A 1 19 ASN 19 27 27 ASN ASN A . n A 1 20 TRP 20 28 28 TRP TRP A . n A 1 21 ARG 21 29 29 ARG ARG A . n A 1 22 GLN 22 30 30 GLN GLN A . n A 1 23 ALA 23 31 31 ALA ALA A . n A 1 24 ILE 24 32 32 ILE ILE A . n A 1 25 THR 25 33 33 THR THR A . n A 1 26 GLN 26 34 34 GLN GLN A . n A 1 27 LEU 27 35 35 LEU LEU A . n A 1 28 GLU 28 36 36 GLU GLU A . n A 1 29 ALA 29 37 37 ALA ALA A . n A 1 30 LEU 30 38 38 LEU LEU A . n A 1 31 ASP 31 39 39 ASP ASP A . n A 1 32 ASN 32 40 40 ASN ASN A . n A 1 33 ARG 33 41 41 ARG ARG A . n A 1 34 TYR 34 42 42 TYR TYR A . n A 1 35 PRO 35 43 43 PRO PRO A . n A 1 36 PHE 36 44 44 PHE PHE A . n A 1 37 GLY 37 45 45 GLY GLY A . n A 1 38 PRO 38 46 46 PRO PRO A . n A 1 39 TYR 39 47 47 TYR TYR A . n A 1 40 SER 40 48 48 SER SER A . n A 1 41 GLN 41 49 49 GLN GLN A . n A 1 42 GLN 42 50 50 GLN GLN A . n A 1 43 VAL 43 51 51 VAL VAL A . n A 1 44 GLN 44 52 52 GLN GLN A . n A 1 45 LEU 45 53 53 LEU LEU A . n A 1 46 ASP 46 54 54 ASP ASP A . n A 1 47 LEU 47 55 55 LEU LEU A . n A 1 48 ILE 48 56 56 ILE ILE A . n A 1 49 TYR 49 57 57 TYR TYR A . n A 1 50 ALA 50 58 58 ALA ALA A . n A 1 51 TYR 51 59 59 TYR TYR A . n A 1 52 TYR 52 60 60 TYR TYR A . n A 1 53 LYS 53 61 61 LYS LYS A . n A 1 54 ASN 54 62 62 ASN ASN A . n A 1 55 ALA 55 63 63 ALA ALA A . n A 1 56 ASP 56 64 64 ASP ASP A . n A 1 57 LEU 57 65 65 LEU LEU A . n A 1 58 PRO 58 66 66 PRO PRO A . n A 1 59 LEU 59 67 67 LEU LEU A . n A 1 60 ALA 60 68 68 ALA ALA A . n A 1 61 GLN 61 69 69 GLN GLN A . n A 1 62 ALA 62 70 70 ALA ALA A . n A 1 63 ALA 63 71 71 ALA ALA A . n A 1 64 ILE 64 72 72 ILE ILE A . n A 1 65 ASP 65 73 73 ASP ASP A . n A 1 66 ARG 66 74 74 ARG ARG A . n A 1 67 PHE 67 75 75 PHE PHE A . n A 1 68 ILE 68 76 76 ILE ILE A . n A 1 69 ARG 69 77 77 ARG ARG A . n A 1 70 LEU 70 78 78 LEU LEU A . n A 1 71 ASN 71 79 79 ASN ASN A . n A 1 72 PRO 72 80 80 PRO PRO A . n A 1 73 THR 73 81 81 THR THR A . n A 1 74 HIS 74 82 82 HIS HIS A . n A 1 75 PRO 75 83 83 PRO PRO A . n A 1 76 ASN 76 84 84 ASN ASN A . n A 1 77 ILE 77 85 85 ILE ILE A . n A 1 78 ASP 78 86 86 ASP ASP A . n A 1 79 TYR 79 87 87 TYR TYR A . n A 1 80 VAL 80 88 88 VAL VAL A . n A 1 81 MET 81 89 89 MET MET A . n A 1 82 TYR 82 90 90 TYR TYR A . n A 1 83 MET 83 91 91 MET MET A . n A 1 84 ARG 84 92 92 ARG ARG A . n A 1 85 GLY 85 93 93 GLY GLY A . n A 1 86 LEU 86 94 94 LEU LEU A . n A 1 87 THR 87 95 95 THR THR A . n A 1 88 ASN 88 96 96 ASN ASN A . n A 1 89 MET 89 97 97 MET MET A . n A 1 90 ALA 90 98 98 ALA ALA A . n A 1 91 LEU 91 99 99 LEU LEU A . n A 1 92 ASP 92 100 100 ASP ASP A . n A 1 93 ASP 93 101 101 ASP ASP A . n A 1 94 SER 94 102 ? ? ? A . n A 1 95 ALA 95 103 ? ? ? A . n A 1 96 LEU 96 104 ? ? ? A . n A 1 97 GLN 97 105 ? ? ? A . n A 1 98 GLY 98 106 ? ? ? A . n A 1 99 PHE 99 107 ? ? ? A . n A 1 100 PHE 100 108 ? ? ? A . n A 1 101 GLY 101 109 ? ? ? A . n A 1 102 VAL 102 110 ? ? ? A . n A 1 103 ASP 103 111 ? ? ? A . n A 1 104 ARG 104 112 ? ? ? A . n A 1 105 SER 105 113 ? ? ? A . n A 1 106 ASP 106 114 ? ? ? A . n A 1 107 ARG 107 115 ? ? ? A . n A 1 108 ASP 108 116 116 ASP ASP A . n A 1 109 PRO 109 117 117 PRO PRO A . n A 1 110 GLN 110 118 118 GLN GLN A . n A 1 111 GLN 111 119 119 GLN GLN A . n A 1 112 ALA 112 120 120 ALA ALA A . n A 1 113 ARG 113 121 121 ARG ARG A . n A 1 114 ALA 114 122 122 ALA ALA A . n A 1 115 ALA 115 123 123 ALA ALA A . n A 1 116 PHE 116 124 124 PHE PHE A . n A 1 117 SER 117 125 125 SER SER A . n A 1 118 ASP 118 126 126 ASP ASP A . n A 1 119 PHE 119 127 127 PHE PHE A . n A 1 120 SER 120 128 128 SER SER A . n A 1 121 LYS 121 129 129 LYS LYS A . n A 1 122 LEU 122 130 130 LEU LEU A . n A 1 123 VAL 123 131 131 VAL VAL A . n A 1 124 ARG 124 132 132 ARG ARG A . n A 1 125 GLY 125 133 133 GLY GLY A . n A 1 126 TYR 126 134 134 TYR TYR A . n A 1 127 PRO 127 135 135 PRO PRO A . n A 1 128 ASN 128 136 136 ASN ASN A . n A 1 129 SER 129 137 137 SER SER A . n A 1 130 GLN 130 138 138 GLN GLN A . n A 1 131 TYR 131 139 139 TYR TYR A . n A 1 132 THR 132 140 140 THR THR A . n A 1 133 THR 133 141 141 THR THR A . n A 1 134 ASP 134 142 142 ASP ASP A . n A 1 135 ALA 135 143 143 ALA ALA A . n A 1 136 THR 136 144 144 THR THR A . n A 1 137 LYS 137 145 145 LYS LYS A . n A 1 138 ARG 138 146 146 ARG ARG A . n A 1 139 LEU 139 147 147 LEU LEU A . n A 1 140 VAL 140 148 148 VAL VAL A . n A 1 141 PHE 141 149 149 PHE PHE A . n A 1 142 LEU 142 150 150 LEU LEU A . n A 1 143 LYS 143 151 151 LYS LYS A . n A 1 144 ASP 144 152 152 ASP ASP A . n A 1 145 ARG 145 153 153 ARG ARG A . n A 1 146 LEU 146 154 154 LEU LEU A . n A 1 147 ALA 147 155 155 ALA ALA A . n A 1 148 LYS 148 156 156 LYS LYS A . n A 1 149 TYR 149 157 157 TYR TYR A . n A 1 150 GLU 150 158 158 GLU GLU A . n A 1 151 TYR 151 159 159 TYR TYR A . n A 1 152 SER 152 160 160 SER SER A . n A 1 153 VAL 153 161 161 VAL VAL A . n A 1 154 ALA 154 162 162 ALA ALA A . n A 1 155 GLU 155 163 163 GLU GLU A . n A 1 156 TYR 156 164 164 TYR TYR A . n A 1 157 TYR 157 165 165 TYR TYR A . n A 1 158 THR 158 166 166 THR THR A . n A 1 159 GLU 159 167 167 GLU GLU A . n A 1 160 ARG 160 168 168 ARG ARG A . n A 1 161 GLY 161 169 169 GLY GLY A . n A 1 162 ALA 162 170 170 ALA ALA A . n A 1 163 TRP 163 171 171 TRP TRP A . n A 1 164 VAL 164 172 172 VAL VAL A . n A 1 165 ALA 165 173 173 ALA ALA A . n A 1 166 VAL 166 174 174 VAL VAL A . n A 1 167 VAL 167 175 175 VAL VAL A . n A 1 168 ASN 168 176 176 ASN ASN A . n A 1 169 ARG 169 177 177 ARG ARG A . n A 1 170 VAL 170 178 178 VAL VAL A . n A 1 171 GLU 171 179 179 GLU GLU A . n A 1 172 GLY 172 180 180 GLY GLY A . n A 1 173 MET 173 181 181 MET MET A . n A 1 174 LEU 174 182 182 LEU LEU A . n A 1 175 ARG 175 183 183 ARG ARG A . n A 1 176 ASP 176 184 184 ASP ASP A . n A 1 177 TYR 177 185 185 TYR TYR A . n A 1 178 PRO 178 186 186 PRO PRO A . n A 1 179 ASP 179 187 187 ASP ASP A . n A 1 180 THR 180 188 188 THR THR A . n A 1 181 GLN 181 189 189 GLN GLN A . n A 1 182 ALA 182 190 190 ALA ALA A . n A 1 183 THR 183 191 191 THR THR A . n A 1 184 ARG 184 192 192 ARG ARG A . n A 1 185 ASP 185 193 193 ASP ASP A . n A 1 186 ALA 186 194 194 ALA ALA A . n A 1 187 LEU 187 195 195 LEU LEU A . n A 1 188 PRO 188 196 196 PRO PRO A . n A 1 189 LEU 189 197 197 LEU LEU A . n A 1 190 MET 190 198 198 MET MET A . n A 1 191 GLU 191 199 199 GLU GLU A . n A 1 192 ASN 192 200 200 ASN ASN A . n A 1 193 ALA 193 201 201 ALA ALA A . n A 1 194 TYR 194 202 202 TYR TYR A . n A 1 195 ARG 195 203 203 ARG ARG A . n A 1 196 GLN 196 204 204 GLN GLN A . n A 1 197 MET 197 205 205 MET MET A . n A 1 198 GLN 198 206 206 GLN GLN A . n A 1 199 MET 199 207 207 MET MET A . n A 1 200 ASN 200 208 208 ASN ASN A . n A 1 201 ALA 201 209 209 ALA ALA A . n A 1 202 GLN 202 210 210 GLN GLN A . n A 1 203 ALA 203 211 211 ALA ALA A . n A 1 204 GLU 204 212 212 GLU GLU A . n A 1 205 LYS 205 213 213 LYS LYS A . n A 1 206 VAL 206 214 214 VAL VAL A . n A 1 207 ALA 207 215 215 ALA ALA A . n A 1 208 LYS 208 216 216 LYS LYS A . n A 1 209 ILE 209 217 217 ILE ILE A . n A 1 210 ILE 210 218 218 ILE ILE A . n A 1 211 ALA 211 219 219 ALA ALA A . n A 1 212 ALA 212 220 220 ALA ALA A . n A 1 213 ASN 213 221 221 ASN ASN A . n A 1 214 SER 214 222 222 SER SER A . n A 1 215 SER 215 223 223 SER SER A . n A 1 216 ASN 216 224 224 ASN ASN A . n A 1 217 THR 217 225 225 THR THR A . n A 1 218 LEU 218 226 226 LEU LEU A . n A 1 219 GLU 219 227 227 GLU GLU A . n A 1 220 HIS 220 228 228 HIS HIS A . n A 1 221 HIS 221 229 229 HIS HIS A . n A 1 222 HIS 222 230 230 HIS HIS A . n A 1 223 HIS 223 231 231 HIS HIS A . n A 1 224 HIS 224 232 232 HIS HIS A . n A 1 225 HIS 225 233 233 HIS HIS A . n # 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 URE 1 1234 1234 URE URE A . C 3 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . C 3 HOH 20 2020 2020 HOH HOH A . C 3 HOH 21 2021 2021 HOH HOH A . C 3 HOH 22 2022 2022 HOH HOH A . C 3 HOH 23 2023 2023 HOH HOH A . C 3 HOH 24 2024 2024 HOH HOH A . C 3 HOH 25 2025 2025 HOH HOH A . C 3 HOH 26 2026 2026 HOH HOH A . C 3 HOH 27 2027 2027 HOH HOH A . C 3 HOH 28 2028 2028 HOH HOH A . C 3 HOH 29 2029 2029 HOH HOH A . C 3 HOH 30 2030 2030 HOH HOH A . C 3 HOH 31 2031 2031 HOH HOH A . C 3 HOH 32 2032 2032 HOH HOH A . C 3 HOH 33 2033 2033 HOH HOH A . C 3 HOH 34 2034 2034 HOH HOH A . C 3 HOH 35 2035 2035 HOH HOH A . C 3 HOH 36 2036 2036 HOH HOH A . C 3 HOH 37 2037 2037 HOH HOH A . C 3 HOH 38 2038 2038 HOH HOH A . C 3 HOH 39 2039 2039 HOH HOH A . C 3 HOH 40 2040 2040 HOH HOH A . C 3 HOH 41 2041 2041 HOH HOH A . C 3 HOH 42 2042 2042 HOH HOH A . C 3 HOH 43 2043 2043 HOH HOH A . C 3 HOH 44 2044 2044 HOH HOH A . C 3 HOH 45 2045 2045 HOH HOH A . C 3 HOH 46 2046 2046 HOH HOH A . C 3 HOH 47 2047 2047 HOH HOH A . C 3 HOH 48 2048 2048 HOH HOH A . C 3 HOH 49 2049 2049 HOH HOH A . C 3 HOH 50 2050 2050 HOH HOH A . C 3 HOH 51 2051 2051 HOH HOH A . C 3 HOH 52 2052 2052 HOH HOH A . C 3 HOH 53 2053 2053 HOH HOH A . C 3 HOH 54 2054 2054 HOH HOH A . C 3 HOH 55 2055 2055 HOH HOH A . C 3 HOH 56 2056 2056 HOH HOH A . C 3 HOH 57 2057 2057 HOH HOH A . C 3 HOH 58 2058 2058 HOH HOH A . C 3 HOH 59 2059 2059 HOH HOH A . C 3 HOH 60 2060 2060 HOH HOH A . C 3 HOH 61 2061 2061 HOH HOH A . C 3 HOH 62 2062 2062 HOH HOH A . C 3 HOH 63 2063 2063 HOH HOH A . C 3 HOH 64 2064 2064 HOH HOH A . C 3 HOH 65 2065 2065 HOH HOH A . C 3 HOH 66 2066 2066 HOH HOH A . C 3 HOH 67 2067 2067 HOH HOH A . C 3 HOH 68 2068 2068 HOH HOH A . C 3 HOH 69 2069 2069 HOH HOH A . C 3 HOH 70 2070 2070 HOH HOH A . C 3 HOH 71 2071 2071 HOH HOH A . C 3 HOH 72 2072 2072 HOH HOH A . C 3 HOH 73 2073 2073 HOH HOH A . C 3 HOH 74 2074 2074 HOH HOH A . C 3 HOH 75 2075 2075 HOH HOH A . C 3 HOH 76 2076 2076 HOH HOH A . C 3 HOH 77 2077 2077 HOH HOH A . C 3 HOH 78 2078 2078 HOH HOH A . C 3 HOH 79 2079 2079 HOH HOH A . C 3 HOH 80 2080 2080 HOH HOH A . C 3 HOH 81 2081 2081 HOH HOH A . C 3 HOH 82 2082 2082 HOH HOH A . C 3 HOH 83 2083 2083 HOH HOH A . C 3 HOH 84 2084 2084 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-06-01 2 'Structure model' 1 1 2011-08-10 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Database references' 2 2 'Structure model' 'Version format compliance' # loop_ _pdbx_refine_tls.pdbx_refine_id _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[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 28.7807 31.1916 6.2709 0.2014 0.0290 0.0906 -0.0399 0.0180 0.0270 4.9656 2.8769 2.7929 0.6217 -0.1348 -0.3655 0.0472 0.2085 0.4499 0.0855 -0.0983 -0.0359 -0.3602 0.2007 0.0511 'X-RAY DIFFRACTION' 2 ? refined 30.1939 23.0100 10.1827 0.0781 0.0133 0.0513 -0.0275 0.0032 -0.0019 3.7045 1.5557 1.4309 0.5802 0.2684 0.2619 0.0324 -0.0461 -0.0120 0.0721 -0.0173 -0.1105 -0.1893 0.1161 -0.0152 'X-RAY DIFFRACTION' 3 ? refined 26.7608 14.2795 11.5769 0.0631 0.0056 0.0845 -0.0074 0.0068 0.0121 3.8546 1.1959 3.1862 0.2014 1.2340 0.4032 0.1114 -0.1036 -0.3696 0.0263 -0.0077 -0.1107 0.1565 0.0310 -0.1037 'X-RAY DIFFRACTION' 4 ? refined 15.7440 12.0643 16.9061 0.0665 0.1045 0.0987 -0.0241 0.0352 0.0424 7.5401 3.0223 3.6888 3.6334 0.7361 0.3104 0.0437 -0.6024 -0.5293 -0.0239 -0.1352 -0.2152 0.1388 -0.1412 0.0915 'X-RAY DIFFRACTION' 5 ? refined 1.6043 -0.9952 14.6290 0.0424 0.1627 0.0946 -0.0534 0.0300 -0.0233 2.9072 5.2930 0.6654 3.6010 0.8582 0.9480 -0.1410 0.0776 0.0458 -0.2747 0.1502 0.0220 -0.0948 0.0610 -0.0092 'X-RAY DIFFRACTION' 6 ? refined -2.0928 -3.4566 25.8886 0.0762 0.2031 0.1274 -0.0383 0.0214 -0.0130 1.7010 1.8520 2.4916 1.4079 1.6358 1.4326 0.0688 -0.2454 0.0664 0.2088 -0.1162 -0.0066 -0.0401 -0.2235 0.0475 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_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.selection_details 'X-RAY DIFFRACTION' 1 1 A 11 ? ? A 40 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 41 ? ? A 62 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 63 ? ? A 84 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 85 ? ? A 140 ? ? ? ? 'X-RAY DIFFRACTION' 5 5 A 141 ? ? A 184 ? ? ? ? 'X-RAY DIFFRACTION' 6 6 A 185 ? ? A 233 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.5.0071 ? 1 XDS 'data reduction' . ? 2 XDS 'data scaling' . ? 3 SHARP phasing . ? 4 DM phasing . ? 5 BUCCANEER phasing . ? 6 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OE2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 GLU _pdbx_validate_close_contact.auth_seq_id_1 199 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 NH1 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ARG _pdbx_validate_close_contact.auth_seq_id_2 203 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.92 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CA _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 THR _pdbx_validate_rmsd_bond.auth_seq_id_1 140 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 B _pdbx_validate_rmsd_bond.auth_atom_id_2 CB _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 THR _pdbx_validate_rmsd_bond.auth_seq_id_2 140 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 B _pdbx_validate_rmsd_bond.bond_value 1.694 _pdbx_validate_rmsd_bond.bond_target_value 1.529 _pdbx_validate_rmsd_bond.bond_deviation 0.165 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.026 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A LEU 147 ? ? CG A LEU 147 ? ? CD1 A LEU 147 ? ? 123.58 111.00 12.58 1.70 N 2 1 NE A ARG 203 ? ? CZ A ARG 203 ? ? NH1 A ARG 203 ? ? 115.65 120.30 -4.65 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 THR A 140 ? ? -29.13 -61.89 2 1 HIS A 228 ? ? -144.74 24.60 # 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 ASP 9 ? A ASP 1 2 1 Y 1 A ASN 10 ? A ASN 2 3 1 Y 1 A SER 102 ? A SER 94 4 1 Y 1 A ALA 103 ? A ALA 95 5 1 Y 1 A LEU 104 ? A LEU 96 6 1 Y 1 A GLN 105 ? A GLN 97 7 1 Y 1 A GLY 106 ? A GLY 98 8 1 Y 1 A PHE 107 ? A PHE 99 9 1 Y 1 A PHE 108 ? A PHE 100 10 1 Y 1 A GLY 109 ? A GLY 101 11 1 Y 1 A VAL 110 ? A VAL 102 12 1 Y 1 A ASP 111 ? A ASP 103 13 1 Y 1 A ARG 112 ? A ARG 104 14 1 Y 1 A SER 113 ? A SER 105 15 1 Y 1 A ASP 114 ? A ASP 106 16 1 Y 1 A ARG 115 ? A ARG 107 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 UREA URE 3 water HOH #