data_2KKD # _entry.id 2KKD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2KKD pdb_00002kkd 10.2210/pdb2kkd/pdb RCSB RCSB101228 ? ? WWPDB D_1000101228 ? ? # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2010-01-26 _pdbx_database_PDB_obs_spr.pdb_id 2KKD _pdbx_database_PDB_obs_spr.replace_pdb_id 2QKZ _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 8RXN PDB 'X-ray stucture of same protein but with native Fe centre' unspecified 2QL0 PDB 'NMR stucture of the Zn substituted form of the same protein' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KKD _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-06-18 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nunes, S.G.' 1 'Volkman, B.F.' 2 'Moura, J.J.G.' 3 'Moura, I.' 4 'Macedo, A.L.' 5 'Markley, J.L.' 6 'Duarte, I.C.' 7 # _citation.id primary _citation.title 'An NMR structural study of nickel-substituted rubredoxin' _citation.journal_abbrev J.Biol.Inorg.Chem. _citation.journal_volume 15 _citation.page_first 409 _citation.page_last 420 _citation.year 2010 _citation.journal_id_ASTM JJBCFA _citation.country GW _citation.journal_id_ISSN 0949-8257 _citation.journal_id_CSD 2154 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19997764 _citation.pdbx_database_id_DOI 10.1007/s00775-009-0613-6 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Goodfellow, B.J.' 1 ? primary 'Duarte, I.C.' 2 ? primary 'Macedo, A.L.' 3 ? primary 'Volkman, B.F.' 4 ? primary 'Nunes, S.G.' 5 ? primary 'Moura, I.' 6 ? primary 'Markley, J.L.' 7 ? primary 'Moura, J.J.' 8 ? # 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 Rubredoxin 5578.174 1 ? ? ? ? 2 non-polymer syn 'NICKEL (II) ION' 58.693 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Rd # _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 MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA _entity_poly.pdbx_seq_one_letter_code_can MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA _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 MET n 1 2 LYS n 1 3 LYS n 1 4 TYR n 1 5 VAL n 1 6 CYS n 1 7 THR n 1 8 VAL n 1 9 CYS n 1 10 GLY n 1 11 TYR n 1 12 GLU n 1 13 TYR n 1 14 ASP n 1 15 PRO n 1 16 ALA n 1 17 GLU n 1 18 GLY n 1 19 ASP n 1 20 PRO n 1 21 ASP n 1 22 ASN n 1 23 GLY n 1 24 VAL n 1 25 LYS n 1 26 PRO n 1 27 GLY n 1 28 THR n 1 29 SER n 1 30 PHE n 1 31 ASP n 1 32 ASP n 1 33 LEU n 1 34 PRO n 1 35 ALA n 1 36 ASP n 1 37 TRP n 1 38 VAL n 1 39 CYS n 1 40 PRO n 1 41 VAL n 1 42 CYS n 1 43 GLY n 1 44 ALA n 1 45 PRO n 1 46 LYS n 1 47 SER n 1 48 GLU n 1 49 PHE n 1 50 GLU n 1 51 ALA n 1 52 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 ? _entity_src_gen.pdbx_gene_src_gene 'rub, DVU_3184' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'Hidenborough/ATCC 29579/NCIMB 8303' _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 'Desulfovibrio vulgaris str. Hildenborough' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 882 _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 pT7-7 _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 RUBR_DESVH _struct_ref.pdbx_db_accession P00269 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA _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 2KKD _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 52 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00269 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 52 _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 52 # 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 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 NI non-polymer . 'NICKEL (II) ION' ? 'Ni 2' 58.693 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '3D 1H-15N NOESY' 1 2 1 '3D 1H-15N TOCSY' 1 3 1 '2D 1H-15N HSQC' 1 4 2 '2D 1H-1H NOESY' 1 5 2 '2D 1H-1H TOCSY' 1 6 2 '2D NOESY with fast recycle' 1 7 3 '1D NOE difference with super-WEFT' 1 8 3 '2D NOESY with fast recycle' 1 9 3 '2D 1H-1H NOESY' 1 10 3 '2D 1H-1H TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.05 _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 296 _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 '50 mM sodium phosphate-1, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' '50 mM sodium phosphate-2, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '2 mM sodium azide-3, 100% D2O' 3 '100% 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 DRX 1 'Bruker DRX' 600 Bruker DRX 2 'Bruker DRX' # _pdbx_nmr_refine.entry_id 2KKD _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details 'structure refinement used pseudocontact shifts' _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 'target function' _pdbx_nmr_ensemble.conformers_calculated_total_number 400 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KKD _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 2KKD _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_software.authors 'Guntert P.' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name CYANA _pdbx_nmr_software.version ? _pdbx_nmr_software.ordinal 1 # _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 2KKD _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KKD _struct.title 'NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin' _struct.pdbx_model_details 'closest to the average, model 6' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KKD _struct_keywords.pdbx_keywords 'ELECTRON TRANSPORT' _struct_keywords.text 'electron transport, [Fe-4S], iron, metal-binding, Cytoplasm, Transport' # 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 SER A 29 ? LEU A 33 ? SER A 29 LEU A 33 5 ? 5 HELX_P HELX_P2 2 PRO A 45 ? SER A 47 ? PRO A 45 SER A 47 5 ? 3 # _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 metalc1 metalc ? ? A CYS 6 SG ? ? ? 1_555 B NI . NI ? ? A CYS 6 A NI 53 1_555 ? ? ? ? ? ? ? 2.417 ? ? metalc2 metalc ? ? A CYS 9 SG ? ? ? 1_555 B NI . NI ? ? A CYS 9 A NI 53 1_555 ? ? ? ? ? ? ? 2.400 ? ? metalc3 metalc ? ? A CYS 39 SG ? ? ? 1_555 B NI . NI ? ? A CYS 39 A NI 53 1_555 ? ? ? ? ? ? ? 2.412 ? ? metalc4 metalc ? ? A CYS 42 SG ? ? ? 1_555 B NI . NI ? ? A CYS 42 A NI 53 1_555 ? ? ? ? ? ? ? 2.397 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense 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 5 ? CYS A 6 ? VAL A 5 CYS A 6 A 2 PHE A 49 ? GLU A 50 ? PHE A 49 GLU A 50 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id VAL _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 5 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id VAL _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 5 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id GLU _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 50 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id GLU _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 50 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id NI _struct_site.pdbx_auth_seq_id 53 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE NI A 53' # 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 5 CYS A 6 ? CYS A 6 . ? 1_555 ? 2 AC1 5 CYS A 9 ? CYS A 9 . ? 1_555 ? 3 AC1 5 CYS A 39 ? CYS A 39 . ? 1_555 ? 4 AC1 5 CYS A 42 ? CYS A 42 . ? 1_555 ? 5 AC1 5 ALA A 44 ? ALA A 44 . ? 1_555 ? # _atom_sites.entry_id 2KKD _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 NI 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 MET 1 1 1 MET MET A . n A 1 2 LYS 2 2 2 LYS LYS A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 TYR 4 4 4 TYR TYR A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 CYS 6 6 6 CYS CYS A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 CYS 9 9 9 CYS CYS A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 TYR 11 11 11 TYR TYR A . n A 1 12 GLU 12 12 12 GLU GLU A . n A 1 13 TYR 13 13 13 TYR TYR A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 PRO 15 15 15 PRO PRO A . n A 1 16 ALA 16 16 16 ALA ALA A . n A 1 17 GLU 17 17 17 GLU GLU A . n A 1 18 GLY 18 18 18 GLY GLY A . n A 1 19 ASP 19 19 19 ASP ASP A . n A 1 20 PRO 20 20 20 PRO PRO A . n A 1 21 ASP 21 21 21 ASP ASP A . n A 1 22 ASN 22 22 22 ASN ASN A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 VAL 24 24 24 VAL VAL A . n A 1 25 LYS 25 25 25 LYS LYS A . n A 1 26 PRO 26 26 26 PRO PRO A . n A 1 27 GLY 27 27 27 GLY GLY A . n A 1 28 THR 28 28 28 THR THR A . n A 1 29 SER 29 29 29 SER SER A . n A 1 30 PHE 30 30 30 PHE PHE A . n A 1 31 ASP 31 31 31 ASP ASP A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 LEU 33 33 33 LEU LEU A . n A 1 34 PRO 34 34 34 PRO PRO A . n A 1 35 ALA 35 35 35 ALA ALA A . n A 1 36 ASP 36 36 36 ASP ASP A . n A 1 37 TRP 37 37 37 TRP TRP A . n A 1 38 VAL 38 38 38 VAL VAL A . n A 1 39 CYS 39 39 39 CYS CYS A . n A 1 40 PRO 40 40 40 PRO PRO A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 CYS 42 42 42 CYS CYS A . n A 1 43 GLY 43 43 43 GLY GLY A . n A 1 44 ALA 44 44 44 ALA ALA A . n A 1 45 PRO 45 45 45 PRO PRO A . n A 1 46 LYS 46 46 46 LYS LYS A . n A 1 47 SER 47 47 47 SER SER A . n A 1 48 GLU 48 48 48 GLU GLU A . n A 1 49 PHE 49 49 49 PHE PHE A . n A 1 50 GLU 50 50 50 GLU GLU A . n A 1 51 ALA 51 51 51 ALA ALA A . n A 1 52 ALA 52 52 52 ALA ALA A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id NI _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 53 _pdbx_nonpoly_scheme.auth_seq_num 53 _pdbx_nonpoly_scheme.pdb_mon_id NI _pdbx_nonpoly_scheme.auth_mon_id NI _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 SG ? A CYS 6 ? A CYS 6 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 9 ? A CYS 9 ? 1_555 112.8 ? 2 SG ? A CYS 6 ? A CYS 6 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 39 ? A CYS 39 ? 1_555 111.4 ? 3 SG ? A CYS 9 ? A CYS 9 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 39 ? A CYS 39 ? 1_555 94.4 ? 4 SG ? A CYS 6 ? A CYS 6 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 42 ? A CYS 42 ? 1_555 111.3 ? 5 SG ? A CYS 9 ? A CYS 9 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 42 ? A CYS 42 ? 1_555 113.3 ? 6 SG ? A CYS 39 ? A CYS 39 ? 1_555 NI ? B NI . ? A NI 53 ? 1_555 SG ? A CYS 42 ? A CYS 42 ? 1_555 112.6 ? # 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 2009-12-22 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Database references' 3 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_struct_assembly 3 3 'Structure model' pdbx_struct_conn_angle 4 3 'Structure model' pdbx_struct_oper_list 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.value' 8 3 'Structure model' '_struct_conn.pdbx_dist_value' 9 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 12 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 13 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 'sodium phosphate-1' 50 ? mM ? 1 'sodium phosphate-2' 50 ? mM ? 2 'sodium azide-3' 2 ? 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 2 O A PRO 45 ? ? H A GLU 48 ? ? 1.59 2 4 O A PRO 45 ? ? H A GLU 48 ? ? 1.47 3 4 H A CYS 6 ? ? O A GLY 10 ? ? 1.54 4 4 H A THR 7 ? ? O A GLU 48 ? ? 1.58 5 5 O A VAL 5 ? ? HG1 A THR 7 ? ? 1.42 6 5 O A PRO 45 ? ? H A GLU 48 ? ? 1.57 7 6 O A PRO 45 ? ? H A GLU 48 ? ? 1.49 8 7 O A PRO 45 ? ? H A GLU 48 ? ? 1.52 9 8 O A ASP 14 ? ? H A GLY 18 ? ? 1.54 10 9 O A ASP 14 ? ? H A GLY 18 ? ? 1.58 11 11 O A ASP 14 ? ? H A GLY 18 ? ? 1.60 12 12 O A PRO 45 ? ? H A GLU 48 ? ? 1.55 13 12 O A PRO 20 ? ? H A GLY 23 ? ? 1.59 14 14 O A PRO 45 ? ? H A GLU 48 ? ? 1.58 15 15 O A ASP 14 ? ? H A GLY 18 ? ? 1.55 # 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 3 ? ? -40.62 108.44 2 1 THR A 7 ? ? -104.82 43.06 3 1 VAL A 8 ? ? -148.18 -45.50 4 1 CYS A 9 ? ? -122.35 -50.87 5 1 ASP A 19 ? ? -174.15 108.70 6 1 LEU A 33 ? ? -47.51 157.33 7 1 CYS A 39 ? ? -43.26 103.23 8 1 VAL A 41 ? ? -145.79 -45.24 9 1 ALA A 44 ? ? -25.86 142.34 10 2 LYS A 2 ? ? 84.39 -168.30 11 2 LYS A 3 ? ? 63.31 115.77 12 2 THR A 7 ? ? 71.30 36.85 13 2 VAL A 8 ? ? -152.56 -45.38 14 2 CYS A 39 ? ? -38.54 104.87 15 2 PRO A 40 ? ? -74.98 44.67 16 2 VAL A 41 ? ? -136.48 -57.87 17 3 THR A 7 ? ? 80.10 29.63 18 3 VAL A 8 ? ? -146.35 -44.81 19 3 TYR A 11 ? ? -162.65 111.04 20 3 ASP A 19 ? ? -179.95 121.91 21 3 LEU A 33 ? ? -46.55 153.36 22 3 CYS A 39 ? ? -38.75 104.37 23 3 PRO A 40 ? ? -75.05 42.52 24 3 VAL A 41 ? ? -133.42 -53.61 25 4 LYS A 2 ? ? 87.25 -149.03 26 4 LYS A 3 ? ? 63.30 117.69 27 4 THR A 7 ? ? -94.37 40.63 28 4 VAL A 8 ? ? -145.44 -43.18 29 4 CYS A 9 ? ? -128.24 -50.42 30 4 TYR A 11 ? ? 35.22 92.26 31 4 ASP A 19 ? ? -176.08 108.98 32 4 LEU A 33 ? ? -39.76 150.27 33 4 CYS A 39 ? ? -40.95 104.19 34 4 PRO A 40 ? ? -75.05 49.45 35 4 VAL A 41 ? ? -144.22 -59.11 36 5 LYS A 2 ? ? -77.11 -169.78 37 5 LYS A 3 ? ? 68.83 116.25 38 5 VAL A 8 ? ? -143.30 -45.59 39 5 CYS A 9 ? ? -123.40 -50.08 40 5 TYR A 11 ? ? -169.63 104.69 41 5 ASP A 19 ? ? 179.58 121.00 42 5 CYS A 39 ? ? -37.34 104.94 43 5 PRO A 40 ? ? -75.01 46.52 44 5 VAL A 41 ? ? -138.62 -52.63 45 6 LYS A 3 ? ? 69.45 121.00 46 6 VAL A 8 ? ? -65.00 -83.40 47 6 GLU A 12 ? ? -35.61 118.51 48 6 ASP A 19 ? ? -176.90 108.85 49 6 CYS A 39 ? ? -39.95 104.76 50 6 VAL A 41 ? ? -147.24 -52.26 51 6 PHE A 49 ? ? -35.31 136.50 52 7 THR A 7 ? ? -86.90 -76.49 53 7 TYR A 11 ? ? 55.56 114.99 54 7 ASP A 19 ? ? -179.52 122.72 55 7 CYS A 39 ? ? -40.26 102.73 56 7 VAL A 41 ? ? -144.31 -53.88 57 8 LYS A 2 ? ? 67.12 179.88 58 8 LYS A 3 ? ? -33.47 127.79 59 8 THR A 7 ? ? 80.40 14.68 60 8 VAL A 8 ? ? -130.22 -43.71 61 8 TYR A 11 ? ? -162.79 88.20 62 8 ASP A 19 ? ? -172.70 109.71 63 8 VAL A 38 ? ? 42.69 -165.74 64 8 PRO A 40 ? ? -74.96 48.66 65 8 VAL A 41 ? ? -143.77 -57.79 66 8 ALA A 44 ? ? -24.57 136.27 67 9 TYR A 4 ? ? -103.10 -169.01 68 9 VAL A 8 ? ? -48.52 -73.56 69 9 ASP A 19 ? ? -168.09 108.83 70 9 VAL A 38 ? ? 43.37 -162.16 71 9 PRO A 40 ? ? -75.01 46.21 72 9 VAL A 41 ? ? -140.05 -47.13 73 9 ALA A 44 ? ? -27.00 139.87 74 10 LYS A 2 ? ? -176.35 138.61 75 10 TYR A 4 ? ? -109.64 -169.85 76 10 VAL A 8 ? ? -39.69 -72.64 77 10 CYS A 9 ? ? -97.52 -155.48 78 10 ASP A 19 ? ? -176.23 108.55 79 10 VAL A 38 ? ? 41.83 -160.39 80 10 VAL A 41 ? ? -160.87 -41.23 81 10 ALA A 44 ? ? -25.64 138.35 82 11 THR A 7 ? ? -100.93 41.63 83 11 VAL A 8 ? ? -140.53 -45.05 84 11 CYS A 9 ? ? -123.12 -50.28 85 11 ASP A 19 ? ? 178.32 121.95 86 11 VAL A 38 ? ? 43.04 -165.28 87 11 PRO A 40 ? ? -75.04 47.02 88 11 VAL A 41 ? ? -140.89 -45.83 89 11 ALA A 44 ? ? -28.41 142.35 90 12 TYR A 4 ? ? -103.84 -167.23 91 12 VAL A 8 ? ? -37.82 -70.15 92 12 CYS A 9 ? ? -99.06 -155.48 93 12 ASP A 19 ? ? -178.57 121.71 94 12 LEU A 33 ? ? -45.11 157.18 95 12 CYS A 39 ? ? -37.22 98.42 96 12 VAL A 41 ? ? -158.01 -42.70 97 12 ALA A 44 ? ? 56.88 141.95 98 13 LYS A 3 ? ? 42.15 91.03 99 13 VAL A 8 ? ? -143.14 -46.17 100 13 CYS A 9 ? ? -120.63 -50.77 101 13 ASP A 19 ? ? -178.33 120.34 102 13 CYS A 39 ? ? -44.02 103.40 103 13 VAL A 41 ? ? -146.50 -51.36 104 13 ALA A 44 ? ? -27.79 141.95 105 14 LYS A 2 ? ? 51.67 178.63 106 14 LYS A 3 ? ? 42.27 91.75 107 14 TYR A 4 ? ? -102.25 -169.17 108 14 VAL A 8 ? ? -152.64 -44.03 109 14 TYR A 11 ? ? -168.34 107.94 110 14 ASP A 19 ? ? 177.10 127.42 111 14 PRO A 20 ? ? -74.96 -168.57 112 14 ASP A 21 ? ? 89.52 -35.23 113 14 CYS A 39 ? ? -37.67 103.58 114 14 PRO A 40 ? ? -75.01 45.83 115 14 VAL A 41 ? ? -136.64 -53.92 116 15 LYS A 2 ? ? -55.63 -169.52 117 15 LYS A 3 ? ? 59.58 108.35 118 15 TYR A 11 ? ? 51.48 174.23 119 15 ASP A 19 ? ? -173.31 108.87 120 15 CYS A 39 ? ? -40.01 102.67 121 15 PRO A 40 ? ? -74.96 48.49 122 15 VAL A 41 ? ? -138.39 -49.27 123 15 ALA A 44 ? ? -28.38 144.33 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'NICKEL (II) ION' _pdbx_entity_nonpoly.comp_id NI #