data_2LLZ # _entry.id 2LLZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2LLZ pdb_00002llz 10.2210/pdb2llz/pdb RCSB RCSB102545 ? ? BMRB 18086 ? ? WWPDB D_1000102545 ? ? # _pdbx_database_related.content_type unspecified _pdbx_database_related.db_id 18086 _pdbx_database_related.db_name BMRB _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LLZ _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-11-18 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lord, D.' 1 'Peti, W.' 2 'Page, R.' 3 # _citation.id primary _citation.title 'A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS.' _citation.journal_abbrev Nat.Chem.Biol. _citation.journal_volume 8 _citation.page_first 855 _citation.page_last 861 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1552-4450 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22941047 _citation.pdbx_database_id_DOI 10.1038/nchembio.1062 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, X.' 1 ? primary 'Lord, D.M.' 2 ? primary 'Cheng, H.Y.' 3 ? primary 'Osbourne, D.O.' 4 ? primary 'Hong, S.H.' 5 ? primary 'Sanchez-Torres, V.' 6 ? primary 'Quiroga, C.' 7 ? primary 'Zheng, K.' 8 ? primary 'Herrmann, T.' 9 ? primary 'Peti, W.' 10 ? primary 'Benedik, M.J.' 11 ? primary 'Page, R.' 12 ? primary 'Wood, T.K.' 13 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Uncharacterized protein yjdK' _entity.formula_weight 11672.119 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 ;GHMEGKNKFNTYVVSFDYPSSYSSVFLRLRSLMYDMNFSSIVADEYGIPRQLNENSFAITTSLAASEIEDLIRLKCLDLP DIDFDLNIMTVDDYFRQFYK ; _entity_poly.pdbx_seq_one_letter_code_can ;GHMEGKNKFNTYVVSFDYPSSYSSVFLRLRSLMYDMNFSSIVADEYGIPRQLNENSFAITTSLAASEIEDLIRLKCLDLP DIDFDLNIMTVDDYFRQFYK ; _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 GLY n 1 2 HIS n 1 3 MET n 1 4 GLU n 1 5 GLY n 1 6 LYS n 1 7 ASN n 1 8 LYS n 1 9 PHE n 1 10 ASN n 1 11 THR n 1 12 TYR n 1 13 VAL n 1 14 VAL n 1 15 SER n 1 16 PHE n 1 17 ASP n 1 18 TYR n 1 19 PRO n 1 20 SER n 1 21 SER n 1 22 TYR n 1 23 SER n 1 24 SER n 1 25 VAL n 1 26 PHE n 1 27 LEU n 1 28 ARG n 1 29 LEU n 1 30 ARG n 1 31 SER n 1 32 LEU n 1 33 MET n 1 34 TYR n 1 35 ASP n 1 36 MET n 1 37 ASN n 1 38 PHE n 1 39 SER n 1 40 SER n 1 41 ILE n 1 42 VAL n 1 43 ALA n 1 44 ASP n 1 45 GLU n 1 46 TYR n 1 47 GLY n 1 48 ILE n 1 49 PRO n 1 50 ARG n 1 51 GLN n 1 52 LEU n 1 53 ASN n 1 54 GLU n 1 55 ASN n 1 56 SER n 1 57 PHE n 1 58 ALA n 1 59 ILE n 1 60 THR n 1 61 THR n 1 62 SER n 1 63 LEU n 1 64 ALA n 1 65 ALA n 1 66 SER n 1 67 GLU n 1 68 ILE n 1 69 GLU n 1 70 ASP n 1 71 LEU n 1 72 ILE n 1 73 ARG n 1 74 LEU n 1 75 LYS n 1 76 CYS n 1 77 LEU n 1 78 ASP n 1 79 LEU n 1 80 PRO n 1 81 ASP n 1 82 ILE n 1 83 ASP n 1 84 PHE n 1 85 ASP n 1 86 LEU n 1 87 ASN n 1 88 ILE n 1 89 MET n 1 90 THR n 1 91 VAL n 1 92 ASP n 1 93 ASP n 1 94 TYR n 1 95 PHE n 1 96 ARG n 1 97 GLN n 1 98 PHE n 1 99 TYR n 1 100 LYS 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 'yjdK, b4128, JW4089' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain K12 _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 83333 _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 ? _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 ? _entity_src_gen.pdbx_host_org_vector RP1B _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code YJDK_ECOLI _struct_ref.pdbx_db_accession P0AF61 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MEGKNKFNTYVVSFDYPSSYSSVFLRLRSLMYDMNFSSIVADEYGIPRQLNENSFAITTSLAASEIEDLIRLKCLDLPDI DFDLNIMTVDDYFRQFYK ; _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 2LLZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 100 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0AF61 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 98 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 100 # 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 2LLZ GLY A 1 ? UNP P0AF61 ? ? 'expression tag' 1 1 1 2LLZ HIS A 2 ? UNP P0AF61 ? ? 'expression tag' 2 2 # 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 3 '2D 1H-15N HSQC' 1 2 1 '2D 1H-13C HSQC' 1 3 1 '3D HNCA' 1 4 1 '3D HNCACB' 1 5 1 '3D CBCA(CO)NH' 1 6 1 '3D C(CO)NH' 1 7 1 '3D HBHA(CO)NH' 1 8 1 '3D HCCH-TOCSY' 1 9 3 '3D 1H-15N NOESY' 1 10 1 '3D 1H-13C NOESY' 1 11 2 '2D 1H-1H TOCSY' 1 12 2 '2D 1H-1H NOESY' 1 13 2 '2D 1H-1H COSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 120 _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1.14 mM [U-99% 13C; U-99% 15N] YjdK, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' '1.76 mM YjdK, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 100% D2O' 2 '100% D2O' '1.42 mM [U-100% 15N] YjdK, 20 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TCEP, 90% H2O/10% D2O' 3 '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker AVANCE 1 'Bruker Avance' 800 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2LLZ _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LLZ _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2LLZ _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger A. T. et.al.' refinement CNS ? 1 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA 2.1 2 Herrmann 'peak picking' UNIO ? 3 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2LLZ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LLZ _struct.title 'GhoS (YjdK) monomer' _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LLZ _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.text 'RNase, biofilm, UNKNOWN FUNCTION' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _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 PRO A 19 ? SER A 21 ? PRO A 19 SER A 21 5 ? 3 HELX_P HELX_P2 2 TYR A 22 ? MET A 36 ? TYR A 22 MET A 36 1 ? 15 HELX_P HELX_P3 3 ALA A 64 ? LYS A 75 ? ALA A 64 LYS A 75 1 ? 12 HELX_P HELX_P4 4 CYS A 76 ? ASP A 78 ? CYS A 76 ASP A 78 5 ? 3 HELX_P HELX_P5 5 VAL A 91 ? ARG A 96 ? VAL A 91 ARG A 96 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 2 ? # 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 B 1 2 ? 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 PHE A 38 ? SER A 39 ? PHE A 38 SER A 39 A 2 SER A 56 ? ILE A 59 ? SER A 56 ILE A 59 A 3 TYR A 12 ? ASP A 17 ? TYR A 12 ASP A 17 A 4 ASP A 85 ? THR A 90 ? ASP A 85 THR A 90 B 1 ILE A 41 ? ALA A 43 ? ILE A 41 ALA A 43 B 2 PRO A 49 ? GLN A 51 ? PRO A 49 GLN A 51 # 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 SER A 39 ? N SER A 39 O ALA A 58 ? O ALA A 58 A 2 3 O ILE A 59 ? O ILE A 59 N TYR A 12 ? N TYR A 12 A 3 4 N VAL A 13 ? N VAL A 13 O MET A 89 ? O MET A 89 B 1 2 N VAL A 42 ? N VAL A 42 O ARG A 50 ? O ARG A 50 # _atom_sites.entry_id 2LLZ _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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 H 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 GLY 1 1 1 GLY GLY A . n A 1 2 HIS 2 2 2 HIS HIS A . n A 1 3 MET 3 3 3 MET MET A . n A 1 4 GLU 4 4 4 GLU GLU A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 ASN 7 7 7 ASN ASN A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 ASN 10 10 10 ASN ASN A . n A 1 11 THR 11 11 11 THR THR A . n A 1 12 TYR 12 12 12 TYR TYR A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 VAL 14 14 14 VAL VAL A . n A 1 15 SER 15 15 15 SER SER A . n A 1 16 PHE 16 16 16 PHE PHE A . n A 1 17 ASP 17 17 17 ASP ASP A . n A 1 18 TYR 18 18 18 TYR TYR A . n A 1 19 PRO 19 19 19 PRO PRO A . n A 1 20 SER 20 20 20 SER SER A . n A 1 21 SER 21 21 21 SER SER A . n A 1 22 TYR 22 22 22 TYR TYR A . n A 1 23 SER 23 23 23 SER SER A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 VAL 25 25 25 VAL VAL A . n A 1 26 PHE 26 26 26 PHE PHE A . n A 1 27 LEU 27 27 27 LEU LEU A . n A 1 28 ARG 28 28 28 ARG ARG A . n A 1 29 LEU 29 29 29 LEU LEU A . n A 1 30 ARG 30 30 30 ARG ARG A . n A 1 31 SER 31 31 31 SER SER A . n A 1 32 LEU 32 32 32 LEU LEU A . n A 1 33 MET 33 33 33 MET MET A . n A 1 34 TYR 34 34 34 TYR TYR A . n A 1 35 ASP 35 35 35 ASP ASP A . n A 1 36 MET 36 36 36 MET MET A . n A 1 37 ASN 37 37 37 ASN ASN A . n A 1 38 PHE 38 38 38 PHE PHE A . n A 1 39 SER 39 39 39 SER SER A . n A 1 40 SER 40 40 40 SER SER A . n A 1 41 ILE 41 41 41 ILE ILE A . n A 1 42 VAL 42 42 42 VAL VAL A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 ASP 44 44 44 ASP ASP A . n A 1 45 GLU 45 45 45 GLU GLU A . n A 1 46 TYR 46 46 46 TYR TYR A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 ILE 48 48 48 ILE ILE A . n A 1 49 PRO 49 49 49 PRO PRO A . n A 1 50 ARG 50 50 50 ARG ARG A . n A 1 51 GLN 51 51 51 GLN GLN A . n A 1 52 LEU 52 52 52 LEU LEU A . n A 1 53 ASN 53 53 53 ASN ASN A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 ASN 55 55 55 ASN ASN A . n A 1 56 SER 56 56 56 SER SER A . n A 1 57 PHE 57 57 57 PHE PHE A . n A 1 58 ALA 58 58 58 ALA ALA A . n A 1 59 ILE 59 59 59 ILE ILE A . n A 1 60 THR 60 60 60 THR THR A . n A 1 61 THR 61 61 61 THR THR A . n A 1 62 SER 62 62 62 SER SER A . n A 1 63 LEU 63 63 63 LEU LEU A . n A 1 64 ALA 64 64 64 ALA ALA A . n A 1 65 ALA 65 65 65 ALA ALA A . n A 1 66 SER 66 66 66 SER SER A . n A 1 67 GLU 67 67 67 GLU GLU A . n A 1 68 ILE 68 68 68 ILE ILE A . n A 1 69 GLU 69 69 69 GLU GLU A . n A 1 70 ASP 70 70 70 ASP ASP A . n A 1 71 LEU 71 71 71 LEU LEU A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 ARG 73 73 73 ARG ARG A . n A 1 74 LEU 74 74 74 LEU LEU A . n A 1 75 LYS 75 75 75 LYS LYS A . n A 1 76 CYS 76 76 76 CYS CYS A . n A 1 77 LEU 77 77 77 LEU LEU A . n A 1 78 ASP 78 78 78 ASP ASP A . n A 1 79 LEU 79 79 79 LEU LEU A . n A 1 80 PRO 80 80 80 PRO PRO A . n A 1 81 ASP 81 81 81 ASP ASP A . n A 1 82 ILE 82 82 82 ILE ILE A . n A 1 83 ASP 83 83 83 ASP ASP A . n A 1 84 PHE 84 84 84 PHE PHE A . n A 1 85 ASP 85 85 85 ASP ASP A . n A 1 86 LEU 86 86 86 LEU LEU A . n A 1 87 ASN 87 87 87 ASN ASN A . n A 1 88 ILE 88 88 88 ILE ILE A . n A 1 89 MET 89 89 89 MET MET A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 ASP 92 92 92 ASP ASP A . n A 1 93 ASP 93 93 93 ASP ASP A . n A 1 94 TYR 94 94 94 TYR TYR A . n A 1 95 PHE 95 95 95 PHE PHE A . n A 1 96 ARG 96 96 96 ARG ARG A . n A 1 97 GLN 97 97 97 GLN GLN A . n A 1 98 PHE 98 98 98 PHE PHE A . n A 1 99 TYR 99 99 99 TYR TYR A . n A 1 100 LYS 100 100 100 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 2012-09-05 2 'Structure model' 1 1 2012-09-19 3 'Structure model' 1 2 2013-01-16 4 'Structure model' 1 3 2023-06-14 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' Other # 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' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_nmr_spectrometer 4 4 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id YjdK-1 1.14 ? mM '[U-99% 13C; U-99% 15N]' 1 'sodium phosphate-2' 20 ? mM ? 1 'sodium chloride-3' 100 ? mM ? 1 TCEP-4 0.5 ? mM ? 1 YjdK-5 1.76 ? mM ? 2 'sodium phosphate-6' 20 ? mM ? 2 'sodium chloride-7' 100 ? mM ? 2 TCEP-8 0.5 ? mM ? 2 YjdK-9 1.42 ? mM '[U-100% 15N]' 3 'sodium phosphate-10' 20 ? mM ? 3 'sodium chloride-11' 100 ? mM ? 3 TCEP-12 0.5 ? mM ? 3 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 6 OE1 A GLU 4 ? ? HZ2 A LYS 6 ? ? 1.60 2 9 HG1 A THR 90 ? ? OD2 A ASP 93 ? ? 1.58 3 9 O A LEU 52 ? ? H A GLU 54 ? ? 1.58 4 12 HG1 A THR 90 ? ? OD2 A ASP 93 ? ? 1.59 5 16 O A LEU 52 ? ? H A GLU 54 ? ? 1.59 6 20 O A LEU 52 ? ? H A GLU 54 ? ? 1.58 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 3 _pdbx_validate_rmsd_bond.auth_atom_id_1 N _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 60 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CA _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 60 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.330 _pdbx_validate_rmsd_bond.bond_target_value 1.459 _pdbx_validate_rmsd_bond.bond_deviation -0.129 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.020 _pdbx_validate_rmsd_bond.linker_flag 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 LYS A 6 ? ? -102.58 47.47 2 1 TYR A 18 ? ? -175.01 144.59 3 1 MET A 36 ? ? -92.51 -154.33 4 1 ASP A 44 ? ? -79.73 -169.53 5 1 ASN A 53 ? ? -64.99 57.56 6 1 GLU A 54 ? ? -122.14 -55.21 7 1 ASN A 55 ? ? -156.79 -33.42 8 1 THR A 60 ? ? -90.49 30.09 9 1 PRO A 80 ? ? -60.97 -76.30 10 2 MET A 36 ? ? -96.32 -144.91 11 2 ASN A 53 ? ? -66.00 60.99 12 2 ASN A 55 ? ? -174.81 -32.94 13 2 PRO A 80 ? ? -57.57 -76.95 14 2 ASP A 81 ? ? -175.27 142.39 15 2 TYR A 99 ? ? -121.73 -161.41 16 3 MET A 36 ? ? -87.14 -157.48 17 3 ASP A 44 ? ? -79.98 -169.87 18 3 ASN A 53 ? ? -65.64 33.33 19 3 ASN A 55 ? ? 173.46 -27.69 20 3 PRO A 80 ? ? -57.18 -74.81 21 3 ASP A 81 ? ? -170.95 138.35 22 3 TYR A 99 ? ? -79.53 -169.08 23 4 MET A 36 ? ? -92.28 -148.52 24 4 ASP A 44 ? ? -79.58 -158.69 25 4 ASN A 53 ? ? -62.99 22.90 26 4 ASN A 55 ? ? -176.81 -30.00 27 4 PRO A 80 ? ? -60.39 -75.19 28 4 ASP A 81 ? ? -177.19 138.90 29 5 HIS A 2 ? ? -164.78 111.35 30 5 MET A 36 ? ? -93.62 -148.20 31 5 ASP A 44 ? ? -79.65 -166.58 32 5 ASN A 53 ? ? -68.11 55.65 33 5 ASN A 55 ? ? -179.29 -31.46 34 5 THR A 60 ? ? -94.01 31.87 35 5 PRO A 80 ? ? -56.59 -73.08 36 6 MET A 36 ? ? -94.21 -152.06 37 6 ASP A 44 ? ? -79.64 -165.84 38 6 ASN A 53 ? ? -67.10 48.50 39 6 GLU A 54 ? ? -96.67 -60.18 40 6 ASN A 55 ? ? -157.22 4.95 41 6 PRO A 80 ? ? -60.94 -73.85 42 7 MET A 3 ? ? -88.72 35.44 43 7 LYS A 6 ? ? -170.47 148.33 44 7 MET A 36 ? ? -94.87 -152.02 45 7 ASN A 53 ? ? -64.09 23.30 46 7 ASN A 55 ? ? 179.47 -35.52 47 7 PRO A 80 ? ? -54.72 -72.80 48 7 ASP A 81 ? ? -175.99 137.75 49 7 TYR A 94 ? ? -92.03 -60.99 50 8 HIS A 2 ? ? 58.44 75.75 51 8 TYR A 18 ? ? -174.80 148.20 52 8 MET A 36 ? ? -94.37 -153.69 53 8 ASN A 53 ? ? -69.19 61.94 54 8 GLU A 54 ? ? -121.17 -60.35 55 8 ASN A 55 ? ? -157.19 5.31 56 8 THR A 60 ? ? -94.74 31.95 57 8 PRO A 80 ? ? -59.67 -70.84 58 8 ASP A 81 ? ? -177.10 144.17 59 9 MET A 36 ? ? -88.25 -117.43 60 9 ASN A 53 ? ? -66.26 45.57 61 9 ASN A 55 ? ? 173.29 -27.41 62 9 THR A 60 ? ? -91.33 31.71 63 9 PRO A 80 ? ? -53.92 -73.96 64 9 ASP A 81 ? ? -171.56 131.13 65 9 TYR A 94 ? ? -93.49 -61.70 66 10 LYS A 6 ? ? 176.99 158.39 67 10 MET A 36 ? ? -87.65 -149.63 68 10 ASN A 53 ? ? -61.50 24.10 69 10 ASN A 55 ? ? 175.85 -25.49 70 10 THR A 60 ? ? -99.96 36.54 71 10 PRO A 80 ? ? -60.82 -70.77 72 10 ASP A 81 ? ? 178.18 153.10 73 10 ILE A 82 ? ? -167.66 117.96 74 10 TYR A 99 ? ? -86.65 -158.82 75 11 LYS A 6 ? ? 173.57 126.88 76 11 ASN A 10 ? ? -111.12 -164.67 77 11 MET A 36 ? ? -92.78 -155.98 78 11 ASP A 44 ? ? -79.32 -169.74 79 11 ASN A 53 ? ? -60.81 7.14 80 11 ASN A 55 ? ? -166.51 4.63 81 11 THR A 60 ? ? -98.48 33.30 82 11 PRO A 80 ? ? -55.25 -74.41 83 12 TYR A 18 ? ? -175.45 146.67 84 12 MET A 36 ? ? -94.09 -150.08 85 12 ASP A 44 ? ? -79.97 -169.17 86 12 ASN A 53 ? ? -69.54 49.48 87 12 GLU A 54 ? ? -101.16 -60.07 88 12 ASN A 55 ? ? -153.27 3.13 89 12 PRO A 80 ? ? -58.35 -71.15 90 13 HIS A 2 ? ? 71.52 97.57 91 13 MET A 36 ? ? -90.68 -118.71 92 13 ASN A 53 ? ? -63.40 14.02 93 13 ASN A 55 ? ? -162.46 -34.09 94 13 PRO A 80 ? ? -57.73 -74.16 95 13 ASP A 81 ? ? -171.17 141.29 96 14 HIS A 2 ? ? 73.71 149.35 97 14 MET A 3 ? ? -176.02 91.07 98 14 LYS A 6 ? ? 173.14 113.26 99 14 MET A 36 ? ? -90.84 -157.62 100 14 ASP A 44 ? ? -78.53 -166.33 101 14 ASN A 53 ? ? -64.08 27.50 102 14 ASN A 55 ? ? 178.19 -29.59 103 14 PRO A 80 ? ? -57.14 -76.28 104 14 ASP A 81 ? ? -171.84 127.10 105 15 MET A 36 ? ? -89.01 -155.74 106 15 ASP A 44 ? ? -79.06 -165.57 107 15 ASN A 55 ? ? -164.33 19.32 108 15 THR A 60 ? ? -96.27 34.45 109 15 ASP A 81 ? ? 171.59 140.57 110 16 MET A 36 ? ? -91.97 -154.30 111 16 ASP A 44 ? ? -79.67 -168.38 112 16 ASN A 53 ? ? -67.05 54.72 113 16 ASN A 55 ? ? -164.34 -34.15 114 16 PRO A 80 ? ? -58.93 -76.79 115 17 LYS A 6 ? ? -169.40 101.83 116 17 MET A 36 ? ? -86.94 -159.05 117 17 ASN A 53 ? ? -69.22 58.27 118 17 GLU A 54 ? ? -121.12 -50.82 119 17 ASN A 55 ? ? -156.15 -30.68 120 17 PRO A 80 ? ? -59.53 -75.68 121 17 ASP A 81 ? ? -175.79 127.03 122 18 LYS A 6 ? ? -160.85 112.61 123 18 MET A 36 ? ? -99.04 -154.52 124 18 ASP A 44 ? ? -79.32 -169.82 125 18 PRO A 49 ? ? -67.60 99.42 126 18 ASN A 53 ? ? -64.35 17.32 127 18 ASN A 55 ? ? 179.88 -31.03 128 18 PRO A 80 ? ? -59.14 -72.33 129 18 ASP A 81 ? ? 176.81 141.37 130 19 HIS A 2 ? ? -153.02 80.65 131 19 MET A 36 ? ? -94.18 -154.83 132 19 ASP A 44 ? ? -78.99 -165.72 133 19 ASN A 53 ? ? -68.08 49.15 134 19 ASN A 55 ? ? -164.35 17.94 135 19 THR A 60 ? ? -97.42 34.62 136 19 PRO A 80 ? ? -67.93 -72.30 137 19 ASP A 81 ? ? -176.77 137.09 138 20 TYR A 18 ? ? -172.84 135.53 139 20 MET A 36 ? ? -92.18 -155.01 140 20 ASP A 44 ? ? -78.68 -167.37 141 20 ASN A 53 ? ? -64.09 37.39 142 20 ASN A 55 ? ? -174.96 -33.50 143 20 THR A 60 ? ? -97.11 31.79 144 20 PRO A 80 ? ? -58.71 -74.57 145 20 ASP A 81 ? ? -173.09 127.35 146 20 TYR A 99 ? ? -124.45 -161.42 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 6 ARG A 96 ? ? 0.073 'SIDE CHAIN' 2 7 ARG A 50 ? ? 0.091 'SIDE CHAIN' 3 12 ARG A 50 ? ? 0.073 'SIDE CHAIN' 4 12 ARG A 73 ? ? 0.076 'SIDE CHAIN' 5 13 ARG A 50 ? ? 0.171 'SIDE CHAIN' 6 18 ARG A 50 ? ? 0.141 'SIDE CHAIN' 7 19 ARG A 50 ? ? 0.143 'SIDE CHAIN' #