data_1VYD # _entry.id 1VYD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.294 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1VYD PDBE EBI-15062 WWPDB D_1290015062 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1C2N unspecified 'CYTOCHROME C2, NMR, 20 STRUCTURES' PDB 1C2R unspecified 'CYTOCHROME C2' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1VYD _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2004-04-27 _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 _audit_author.identifier_ORCID 'Dumortier, C.' 1 ? 'Fitch, J.' 2 ? 'Van Petegem, F.' 3 ? 'Vermeulen, W.' 4 ? 'Meyer, T.E.' 5 ? 'Van Beeumen, J.J.' 6 ? 'Cusanovich, M.A.' 7 ? # _citation.id primary _citation.title ;Protein Dynamics in the Region of the Sixth Ligand Methionine Revealed by Studies of Imidazole Binding to Rhodobacter Capsulatus Cytochrome C2 Hinge Mutants. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 7717 _citation.page_last ? _citation.year 2004 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15196014 _citation.pdbx_database_id_DOI 10.1021/BI0362370 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Dumortier, C.' 1 primary 'Fitch, J.' 2 primary 'Van Petegem, F.' 3 primary 'Vermeulen, W.' 4 primary 'Meyer, T.E.' 5 primary 'Van Beeumen, J.J.' 6 primary 'Cusanovich, M.A.' 7 # _cell.entry_id 1VYD _cell.length_a 100.230 _cell.length_b 100.230 _cell.length_c 162.150 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VYD _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 # 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 'CYTOCHROME C2' 12358.074 2 ? YES ? ? 2 non-polymer syn 'PROTOPORPHYRIN IX CONTAINING FE' 616.487 2 ? ? ? ? 3 water nat water 18.015 82 ? ? ? ? # _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 ;GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPG AFLKEKLDDKKAKTEMAFKLAKGGEDVAAYLASVVK ; _entity_poly.pdbx_seq_one_letter_code_can ;GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLYGVVGRTAGTYPEFKYKDSIVALGASGFAWTEEDIATYVKDPG AFLKEKLDDKKAKTEMAFKLAKGGEDVAAYLASVVK ; _entity_poly.pdbx_strand_id A,B _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 ASP n 1 3 ALA n 1 4 ALA n 1 5 LYS n 1 6 GLY n 1 7 GLU n 1 8 LYS n 1 9 GLU n 1 10 PHE n 1 11 ASN n 1 12 LYS n 1 13 CYS n 1 14 LYS n 1 15 THR n 1 16 CYS n 1 17 HIS n 1 18 SER n 1 19 ILE n 1 20 ILE n 1 21 ALA n 1 22 PRO n 1 23 ASP n 1 24 GLY n 1 25 THR n 1 26 GLU n 1 27 ILE n 1 28 VAL n 1 29 LYS n 1 30 GLY n 1 31 ALA n 1 32 LYS n 1 33 THR n 1 34 GLY n 1 35 PRO n 1 36 ASN n 1 37 LEU n 1 38 TYR n 1 39 GLY n 1 40 VAL n 1 41 VAL n 1 42 GLY n 1 43 ARG n 1 44 THR n 1 45 ALA n 1 46 GLY n 1 47 THR n 1 48 TYR n 1 49 PRO n 1 50 GLU n 1 51 PHE n 1 52 LYS n 1 53 TYR n 1 54 LYS n 1 55 ASP n 1 56 SER n 1 57 ILE n 1 58 VAL n 1 59 ALA n 1 60 LEU n 1 61 GLY n 1 62 ALA n 1 63 SER n 1 64 GLY n 1 65 PHE n 1 66 ALA n 1 67 TRP n 1 68 THR n 1 69 GLU n 1 70 GLU n 1 71 ASP n 1 72 ILE n 1 73 ALA n 1 74 THR n 1 75 TYR n 1 76 VAL n 1 77 LYS n 1 78 ASP n 1 79 PRO n 1 80 GLY n 1 81 ALA n 1 82 PHE n 1 83 LEU n 1 84 LYS n 1 85 GLU n 1 86 LYS n 1 87 LEU n 1 88 ASP n 1 89 ASP n 1 90 LYS n 1 91 LYS n 1 92 ALA n 1 93 LYS n 1 94 THR n 1 95 GLU n 1 96 MET n 1 97 ALA n 1 98 PHE n 1 99 LYS n 1 100 LEU n 1 101 ALA n 1 102 LYS n 1 103 GLY n 1 104 GLY n 1 105 GLU n 1 106 ASP n 1 107 VAL n 1 108 ALA n 1 109 ALA n 1 110 TYR n 1 111 LEU n 1 112 ALA n 1 113 SER n 1 114 VAL n 1 115 VAL n 1 116 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 ? _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 'RHODOBACTER CAPSULATUS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1061 _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 ? _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 CY2_RHOCA _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P00094 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1VYD A 1 ? 116 ? P00094 22 ? 137 ? 1 116 2 1 1VYD B 1 ? 116 ? P00094 22 ? 137 ? 1 116 # 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 1VYD GLU A 95 ? UNP P00094 GLY 116 'engineered mutation' 95 1 2 1VYD GLU B 95 ? UNP P00094 GLY 116 'engineered mutation' 95 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HEM non-polymer . 'PROTOPORPHYRIN IX CONTAINING FE' HEME 'C34 H32 Fe N4 O4' 616.487 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1VYD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.17 _exptl_crystal.density_percent_sol 61.21 _exptl_crystal.description ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.50 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'pH 7.50' # _diffrn.id 1 _diffrn.ambient_temp 294.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAC Science DIP-2030' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'NI FILTER' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type NONIUS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1VYD _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 2.300 _reflns.number_obs 12459 _reflns.number_all ? _reflns.percent_possible_obs 88.0 _reflns.pdbx_Rmerge_I_obs 0.08700 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.2700 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1VYD _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 12459 _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 10 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 88 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.198 _refine.ls_R_factor_R_free 0.242 _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 ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'WILD TYPE CYTOCHROME C2' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _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 1736 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 86 _refine_hist.number_atoms_solvent 82 _refine_hist.number_atoms_total 1904 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 10 # _struct_ncs_oper.id 1 _struct_ncs_oper.code given _struct_ncs_oper.details ? _struct_ncs_oper.matrix[1][1] -0.263230 _struct_ncs_oper.matrix[1][2] -0.459150 _struct_ncs_oper.matrix[1][3] -0.848460 _struct_ncs_oper.matrix[2][1] -0.409940 _struct_ncs_oper.matrix[2][2] -0.742890 _struct_ncs_oper.matrix[2][3] 0.529200 _struct_ncs_oper.matrix[3][1] -0.873300 _struct_ncs_oper.matrix[3][2] 0.487120 _struct_ncs_oper.matrix[3][3] 0.007330 _struct_ncs_oper.vector[1] 59.40797 _struct_ncs_oper.vector[2] 98.56004 _struct_ncs_oper.vector[3] 0.79309 # _struct.entry_id 1VYD _struct.title 'Crystal structure of cytochrome C2 mutant G95E' _struct.pdbx_descriptor 'CYTOCHROME C2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1VYD _struct_keywords.pdbx_keywords 'ELECTRON TRANSPORT' _struct_keywords.text 'ELECTRON TRANSPORT, REDOX' # 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # 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 ASP A 2 ? PHE A 10 ? ASP A 2 PHE A 10 1 ? 9 HELX_P HELX_P2 2 ASN A 11 ? CYS A 13 ? ASN A 11 CYS A 13 5 ? 3 HELX_P HELX_P3 3 LYS A 54 ? SER A 63 ? LYS A 54 SER A 63 1 ? 10 HELX_P HELX_P4 4 THR A 68 ? ASP A 78 ? THR A 68 ASP A 78 1 ? 11 HELX_P HELX_P5 5 ASP A 78 ? ASP A 88 ? ASP A 78 ASP A 88 1 ? 11 HELX_P HELX_P6 6 GLY A 103 ? VAL A 114 ? GLY A 103 VAL A 114 1 ? 12 HELX_P HELX_P7 7 ASP B 2 ? LYS B 14 ? ASP B 2 LYS B 14 1 ? 13 HELX_P HELX_P8 8 LYS B 54 ? SER B 63 ? LYS B 54 SER B 63 1 ? 10 HELX_P HELX_P9 9 THR B 68 ? ASP B 78 ? THR B 68 ASP B 78 1 ? 11 HELX_P HELX_P10 10 ASP B 78 ? ASP B 88 ? ASP B 78 ASP B 88 1 ? 11 HELX_P HELX_P11 11 GLY B 103 ? VAL B 114 ? GLY B 103 VAL B 114 1 ? 12 # _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 metalc1 metalc ? ? C HEM . FE ? ? ? 1_555 A HIS 17 NE2 ? ? A HEM 1117 A HIS 17 1_555 ? ? ? ? ? ? ? 2.128 ? metalc2 metalc ? ? C HEM . FE ? ? ? 1_555 A MET 96 SD ? ? A HEM 1117 A MET 96 1_555 ? ? ? ? ? ? ? 2.432 ? metalc3 metalc ? ? D HEM . FE ? ? ? 1_555 B HIS 17 NE2 ? ? B HEM 1117 B HIS 17 1_555 ? ? ? ? ? ? ? 2.172 ? metalc4 metalc ? ? D HEM . FE ? ? ? 1_555 B MET 96 SD ? ? B HEM 1117 B MET 96 1_555 ? ? ? ? ? ? ? 2.468 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? BA ? 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 AA 1 2 ? anti-parallel BA 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 AA 1 ILE A 19 ? ILE A 20 ? ILE A 19 ILE A 20 AA 2 GLU A 26 ? VAL A 28 ? GLU A 26 VAL A 28 BA 1 ILE B 19 ? ILE B 20 ? ILE B 19 ILE B 20 BA 2 GLU B 26 ? VAL B 28 ? GLU B 26 VAL B 28 # 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 AA 1 2 O ILE A 19 ? O ILE A 19 N ILE A 27 ? N ILE A 27 BA 1 2 O ILE B 19 ? O ILE B 19 N ILE B 27 ? N ILE B 27 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 21 'BINDING SITE FOR RESIDUE HEM A 1117' AC2 Software ? ? ? ? 17 'BINDING SITE FOR RESIDUE HEM B 1117' # 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 21 LYS A 12 ? LYS A 12 . ? 1_555 ? 2 AC1 21 CYS A 13 ? CYS A 13 . ? 1_555 ? 3 AC1 21 CYS A 16 ? CYS A 16 . ? 1_555 ? 4 AC1 21 HIS A 17 ? HIS A 17 . ? 1_555 ? 5 AC1 21 LEU A 37 ? LEU A 37 . ? 1_555 ? 6 AC1 21 ARG A 43 ? ARG A 43 . ? 1_555 ? 7 AC1 21 ALA A 45 ? ALA A 45 . ? 1_555 ? 8 AC1 21 GLY A 46 ? GLY A 46 . ? 1_555 ? 9 AC1 21 TYR A 53 ? TYR A 53 . ? 1_555 ? 10 AC1 21 LYS A 54 ? LYS A 54 . ? 1_555 ? 11 AC1 21 ILE A 57 ? ILE A 57 . ? 1_555 ? 12 AC1 21 TRP A 67 ? TRP A 67 . ? 1_555 ? 13 AC1 21 TYR A 75 ? TYR A 75 . ? 1_555 ? 14 AC1 21 VAL A 76 ? VAL A 76 . ? 1_555 ? 15 AC1 21 GLU A 95 ? GLU A 95 . ? 1_555 ? 16 AC1 21 MET A 96 ? MET A 96 . ? 1_555 ? 17 AC1 21 PHE A 98 ? PHE A 98 . ? 1_555 ? 18 AC1 21 HOH E . ? HOH A 2017 . ? 1_555 ? 19 AC1 21 HOH E . ? HOH A 2028 . ? 1_555 ? 20 AC1 21 HOH E . ? HOH A 2038 . ? 1_555 ? 21 AC1 21 HOH E . ? HOH A 2039 . ? 1_555 ? 22 AC2 17 CYS B 13 ? CYS B 13 . ? 1_555 ? 23 AC2 17 CYS B 16 ? CYS B 16 . ? 1_555 ? 24 AC2 17 HIS B 17 ? HIS B 17 . ? 1_555 ? 25 AC2 17 ARG B 43 ? ARG B 43 . ? 1_555 ? 26 AC2 17 ALA B 45 ? ALA B 45 . ? 1_555 ? 27 AC2 17 GLY B 46 ? GLY B 46 . ? 1_555 ? 28 AC2 17 TYR B 53 ? TYR B 53 . ? 1_555 ? 29 AC2 17 LYS B 54 ? LYS B 54 . ? 1_555 ? 30 AC2 17 ILE B 57 ? ILE B 57 . ? 1_555 ? 31 AC2 17 TRP B 67 ? TRP B 67 . ? 1_555 ? 32 AC2 17 TYR B 75 ? TYR B 75 . ? 1_555 ? 33 AC2 17 VAL B 76 ? VAL B 76 . ? 1_555 ? 34 AC2 17 THR B 94 ? THR B 94 . ? 1_555 ? 35 AC2 17 GLU B 95 ? GLU B 95 . ? 1_555 ? 36 AC2 17 MET B 96 ? MET B 96 . ? 1_555 ? 37 AC2 17 PHE B 98 ? PHE B 98 . ? 1_555 ? 38 AC2 17 HOH F . ? HOH B 2043 . ? 1_555 ? # _database_PDB_matrix.entry_id 1VYD _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 1VYD _atom_sites.fract_transf_matrix[1][1] 0.009977 _atom_sites.fract_transf_matrix[1][2] 0.005760 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.011520 _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] 0.006167 _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 FE 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 ASP 2 2 2 ASP ASP A . n A 1 3 ALA 3 3 3 ALA ALA A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 LYS 5 5 5 LYS LYS A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 GLU 7 7 7 GLU GLU A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 GLU 9 9 9 GLU GLU A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 ASN 11 11 11 ASN ASN A . n A 1 12 LYS 12 12 12 LYS LYS A . n A 1 13 CYS 13 13 13 CYS CYS A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 THR 15 15 15 THR THR A . n A 1 16 CYS 16 16 16 CYS CYS A . n A 1 17 HIS 17 17 17 HIS HIS A . n A 1 18 SER 18 18 18 SER SER A . n A 1 19 ILE 19 19 19 ILE ILE A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 PRO 22 22 22 PRO PRO A . n A 1 23 ASP 23 23 23 ASP ASP A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 THR 25 25 25 THR THR A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 ILE 27 27 27 ILE ILE A . n A 1 28 VAL 28 28 28 VAL VAL A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 GLY 30 30 30 GLY GLY A . n A 1 31 ALA 31 31 31 ALA ALA A . n A 1 32 LYS 32 32 32 LYS LYS A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 PRO 35 35 35 PRO PRO A . n A 1 36 ASN 36 36 36 ASN ASN A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 TYR 38 38 38 TYR TYR A . n A 1 39 GLY 39 39 39 GLY GLY A . n A 1 40 VAL 40 40 40 VAL VAL A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 GLY 42 42 42 GLY GLY A . n A 1 43 ARG 43 43 43 ARG ARG A . n A 1 44 THR 44 44 44 THR THR A . n A 1 45 ALA 45 45 45 ALA ALA A . n A 1 46 GLY 46 46 46 GLY GLY A . n A 1 47 THR 47 47 47 THR THR A . n A 1 48 TYR 48 48 48 TYR TYR A . n A 1 49 PRO 49 49 49 PRO PRO A . n A 1 50 GLU 50 50 50 GLU GLU A . n A 1 51 PHE 51 51 51 PHE PHE A . n A 1 52 LYS 52 52 52 LYS LYS A . n A 1 53 TYR 53 53 53 TYR TYR A . n A 1 54 LYS 54 54 54 LYS LYS A . n A 1 55 ASP 55 55 55 ASP ASP A . n A 1 56 SER 56 56 56 SER SER A . n A 1 57 ILE 57 57 57 ILE ILE A . n A 1 58 VAL 58 58 58 VAL VAL A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 GLY 61 61 61 GLY GLY A . n A 1 62 ALA 62 62 62 ALA ALA A . n A 1 63 SER 63 63 63 SER SER A . n A 1 64 GLY 64 64 64 GLY GLY A . n A 1 65 PHE 65 65 65 PHE PHE A . n A 1 66 ALA 66 66 66 ALA ALA A . n A 1 67 TRP 67 67 67 TRP TRP A . n A 1 68 THR 68 68 68 THR THR A . n A 1 69 GLU 69 69 69 GLU GLU A . n A 1 70 GLU 70 70 70 GLU GLU A . n A 1 71 ASP 71 71 71 ASP ASP A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 ALA 73 73 73 ALA ALA A . n A 1 74 THR 74 74 74 THR THR A . n A 1 75 TYR 75 75 75 TYR TYR A . n A 1 76 VAL 76 76 76 VAL VAL A . n A 1 77 LYS 77 77 77 LYS LYS A . n A 1 78 ASP 78 78 78 ASP ASP A . n A 1 79 PRO 79 79 79 PRO PRO A . n A 1 80 GLY 80 80 80 GLY GLY A . n A 1 81 ALA 81 81 81 ALA ALA A . n A 1 82 PHE 82 82 82 PHE PHE A . n A 1 83 LEU 83 83 83 LEU LEU A . n A 1 84 LYS 84 84 84 LYS LYS A . n A 1 85 GLU 85 85 85 GLU GLU A . n A 1 86 LYS 86 86 86 LYS LYS A . n A 1 87 LEU 87 87 87 LEU LEU A . n A 1 88 ASP 88 88 88 ASP ASP A . n A 1 89 ASP 89 89 89 ASP ASP A . n A 1 90 LYS 90 90 90 LYS LYS A . n A 1 91 LYS 91 91 91 LYS LYS A . n A 1 92 ALA 92 92 92 ALA ALA A . n A 1 93 LYS 93 93 93 LYS LYS A . n A 1 94 THR 94 94 94 THR THR A . n A 1 95 GLU 95 95 95 GLU GLU A . n A 1 96 MET 96 96 96 MET MET A . n A 1 97 ALA 97 97 97 ALA ALA A . n A 1 98 PHE 98 98 98 PHE PHE A . n A 1 99 LYS 99 99 99 LYS LYS A . n A 1 100 LEU 100 100 100 LEU LEU A . n A 1 101 ALA 101 101 101 ALA ALA A . n A 1 102 LYS 102 102 102 LYS LYS A . n A 1 103 GLY 103 103 103 GLY GLY A . n A 1 104 GLY 104 104 104 GLY GLY A . n A 1 105 GLU 105 105 105 GLU GLU A . n A 1 106 ASP 106 106 106 ASP ASP A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 ALA 108 108 108 ALA ALA A . n A 1 109 ALA 109 109 109 ALA ALA A . n A 1 110 TYR 110 110 110 TYR TYR A . n A 1 111 LEU 111 111 111 LEU LEU A . n A 1 112 ALA 112 112 112 ALA ALA A . n A 1 113 SER 113 113 113 SER SER A . n A 1 114 VAL 114 114 114 VAL VAL A . n A 1 115 VAL 115 115 115 VAL VAL A . n A 1 116 LYS 116 116 116 LYS LYS A . n B 1 1 GLY 1 1 1 GLY GLY B . n B 1 2 ASP 2 2 2 ASP ASP B . n B 1 3 ALA 3 3 3 ALA ALA B . n B 1 4 ALA 4 4 4 ALA ALA B . n B 1 5 LYS 5 5 5 LYS LYS B . n B 1 6 GLY 6 6 6 GLY GLY B . n B 1 7 GLU 7 7 7 GLU GLU B . n B 1 8 LYS 8 8 8 LYS LYS B . n B 1 9 GLU 9 9 9 GLU GLU B . n B 1 10 PHE 10 10 10 PHE PHE B . n B 1 11 ASN 11 11 11 ASN ASN B . n B 1 12 LYS 12 12 12 LYS LYS B . n B 1 13 CYS 13 13 13 CYS CYS B . n B 1 14 LYS 14 14 14 LYS LYS B . n B 1 15 THR 15 15 15 THR THR B . n B 1 16 CYS 16 16 16 CYS CYS B . n B 1 17 HIS 17 17 17 HIS HIS B . n B 1 18 SER 18 18 18 SER SER B . n B 1 19 ILE 19 19 19 ILE ILE B . n B 1 20 ILE 20 20 20 ILE ILE B . n B 1 21 ALA 21 21 21 ALA ALA B . n B 1 22 PRO 22 22 22 PRO PRO B . n B 1 23 ASP 23 23 23 ASP ASP B . n B 1 24 GLY 24 24 24 GLY GLY B . n B 1 25 THR 25 25 25 THR THR B . n B 1 26 GLU 26 26 26 GLU GLU B . n B 1 27 ILE 27 27 27 ILE ILE B . n B 1 28 VAL 28 28 28 VAL VAL B . n B 1 29 LYS 29 29 29 LYS LYS B . n B 1 30 GLY 30 30 30 GLY GLY B . n B 1 31 ALA 31 31 31 ALA ALA B . n B 1 32 LYS 32 32 32 LYS LYS B . n B 1 33 THR 33 33 33 THR THR B . n B 1 34 GLY 34 34 34 GLY GLY B . n B 1 35 PRO 35 35 35 PRO PRO B . n B 1 36 ASN 36 36 36 ASN ASN B . n B 1 37 LEU 37 37 37 LEU LEU B . n B 1 38 TYR 38 38 38 TYR TYR B . n B 1 39 GLY 39 39 39 GLY GLY B . n B 1 40 VAL 40 40 40 VAL VAL B . n B 1 41 VAL 41 41 41 VAL VAL B . n B 1 42 GLY 42 42 42 GLY GLY B . n B 1 43 ARG 43 43 43 ARG ARG B . n B 1 44 THR 44 44 44 THR THR B . n B 1 45 ALA 45 45 45 ALA ALA B . n B 1 46 GLY 46 46 46 GLY GLY B . n B 1 47 THR 47 47 47 THR THR B . n B 1 48 TYR 48 48 48 TYR TYR B . n B 1 49 PRO 49 49 49 PRO PRO B . n B 1 50 GLU 50 50 50 GLU GLU B . n B 1 51 PHE 51 51 51 PHE PHE B . n B 1 52 LYS 52 52 52 LYS LYS B . n B 1 53 TYR 53 53 53 TYR TYR B . n B 1 54 LYS 54 54 54 LYS LYS B . n B 1 55 ASP 55 55 55 ASP ASP B . n B 1 56 SER 56 56 56 SER SER B . n B 1 57 ILE 57 57 57 ILE ILE B . n B 1 58 VAL 58 58 58 VAL VAL B . n B 1 59 ALA 59 59 59 ALA ALA B . n B 1 60 LEU 60 60 60 LEU LEU B . n B 1 61 GLY 61 61 61 GLY GLY B . n B 1 62 ALA 62 62 62 ALA ALA B . n B 1 63 SER 63 63 63 SER SER B . n B 1 64 GLY 64 64 64 GLY GLY B . n B 1 65 PHE 65 65 65 PHE PHE B . n B 1 66 ALA 66 66 66 ALA ALA B . n B 1 67 TRP 67 67 67 TRP TRP B . n B 1 68 THR 68 68 68 THR THR B . n B 1 69 GLU 69 69 69 GLU GLU B . n B 1 70 GLU 70 70 70 GLU GLU B . n B 1 71 ASP 71 71 71 ASP ASP B . n B 1 72 ILE 72 72 72 ILE ILE B . n B 1 73 ALA 73 73 73 ALA ALA B . n B 1 74 THR 74 74 74 THR THR B . n B 1 75 TYR 75 75 75 TYR TYR B . n B 1 76 VAL 76 76 76 VAL VAL B . n B 1 77 LYS 77 77 77 LYS LYS B . n B 1 78 ASP 78 78 78 ASP ASP B . n B 1 79 PRO 79 79 79 PRO PRO B . n B 1 80 GLY 80 80 80 GLY GLY B . n B 1 81 ALA 81 81 81 ALA ALA B . n B 1 82 PHE 82 82 82 PHE PHE B . n B 1 83 LEU 83 83 83 LEU LEU B . n B 1 84 LYS 84 84 84 LYS LYS B . n B 1 85 GLU 85 85 85 GLU GLU B . n B 1 86 LYS 86 86 86 LYS LYS B . n B 1 87 LEU 87 87 87 LEU LEU B . n B 1 88 ASP 88 88 88 ASP ASP B . n B 1 89 ASP 89 89 89 ASP ASP B . n B 1 90 LYS 90 90 90 LYS LYS B . n B 1 91 LYS 91 91 91 LYS LYS B . n B 1 92 ALA 92 92 92 ALA ALA B . n B 1 93 LYS 93 93 93 LYS LYS B . n B 1 94 THR 94 94 94 THR THR B . n B 1 95 GLU 95 95 95 GLU GLU B . n B 1 96 MET 96 96 96 MET MET B . n B 1 97 ALA 97 97 97 ALA ALA B . n B 1 98 PHE 98 98 98 PHE PHE B . n B 1 99 LYS 99 99 99 LYS LYS B . n B 1 100 LEU 100 100 100 LEU LEU B . n B 1 101 ALA 101 101 101 ALA ALA B . n B 1 102 LYS 102 102 102 LYS LYS B . n B 1 103 GLY 103 103 103 GLY GLY B . n B 1 104 GLY 104 104 104 GLY GLY B . n B 1 105 GLU 105 105 105 GLU GLU B . n B 1 106 ASP 106 106 106 ASP ASP B . n B 1 107 VAL 107 107 107 VAL VAL B . n B 1 108 ALA 108 108 108 ALA ALA B . n B 1 109 ALA 109 109 109 ALA ALA B . n B 1 110 TYR 110 110 110 TYR TYR B . n B 1 111 LEU 111 111 111 LEU LEU B . n B 1 112 ALA 112 112 112 ALA ALA B . n B 1 113 SER 113 113 113 SER SER B . n B 1 114 VAL 114 114 114 VAL VAL B . n B 1 115 VAL 115 115 115 VAL VAL B . n B 1 116 LYS 116 116 116 LYS LYS B . 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 C 2 HEM 1 1117 1117 HEM HEM A . D 2 HEM 1 1117 1117 HEM HEM B . E 3 HOH 1 2001 2001 HOH HOH A . E 3 HOH 2 2002 2002 HOH HOH A . E 3 HOH 3 2003 2003 HOH HOH A . E 3 HOH 4 2004 2004 HOH HOH A . E 3 HOH 5 2005 2005 HOH HOH A . E 3 HOH 6 2006 2006 HOH HOH A . E 3 HOH 7 2007 2007 HOH HOH A . E 3 HOH 8 2008 2008 HOH HOH A . E 3 HOH 9 2009 2009 HOH HOH A . E 3 HOH 10 2010 2010 HOH HOH A . E 3 HOH 11 2011 2011 HOH HOH A . E 3 HOH 12 2012 2012 HOH HOH A . E 3 HOH 13 2013 2013 HOH HOH A . E 3 HOH 14 2014 2014 HOH HOH A . E 3 HOH 15 2015 2015 HOH HOH A . E 3 HOH 16 2016 2016 HOH HOH A . E 3 HOH 17 2017 2017 HOH HOH A . E 3 HOH 18 2018 2018 HOH HOH A . E 3 HOH 19 2019 2019 HOH HOH A . E 3 HOH 20 2020 2020 HOH HOH A . E 3 HOH 21 2021 2021 HOH HOH A . E 3 HOH 22 2022 2022 HOH HOH A . E 3 HOH 23 2023 2023 HOH HOH A . E 3 HOH 24 2024 2024 HOH HOH A . E 3 HOH 25 2025 2025 HOH HOH A . E 3 HOH 26 2026 2026 HOH HOH A . E 3 HOH 27 2027 2027 HOH HOH A . E 3 HOH 28 2028 2028 HOH HOH A . E 3 HOH 29 2029 2029 HOH HOH A . E 3 HOH 30 2030 2030 HOH HOH A . E 3 HOH 31 2031 2031 HOH HOH A . E 3 HOH 32 2032 2032 HOH HOH A . E 3 HOH 33 2033 2033 HOH HOH A . E 3 HOH 34 2034 2034 HOH HOH A . E 3 HOH 35 2035 2035 HOH HOH A . E 3 HOH 36 2036 2036 HOH HOH A . E 3 HOH 37 2037 2037 HOH HOH A . E 3 HOH 38 2038 2038 HOH HOH A . E 3 HOH 39 2039 2039 HOH HOH A . F 3 HOH 1 2001 2001 HOH HOH B . F 3 HOH 2 2002 2002 HOH HOH B . F 3 HOH 3 2003 2003 HOH HOH B . F 3 HOH 4 2004 2004 HOH HOH B . F 3 HOH 5 2005 2005 HOH HOH B . F 3 HOH 6 2006 2006 HOH HOH B . F 3 HOH 7 2007 2007 HOH HOH B . F 3 HOH 8 2008 2008 HOH HOH B . F 3 HOH 9 2009 2009 HOH HOH B . F 3 HOH 10 2010 2010 HOH HOH B . F 3 HOH 11 2011 2011 HOH HOH B . F 3 HOH 12 2012 2012 HOH HOH B . F 3 HOH 13 2013 2013 HOH HOH B . F 3 HOH 14 2014 2014 HOH HOH B . F 3 HOH 15 2015 2015 HOH HOH B . F 3 HOH 16 2016 2016 HOH HOH B . F 3 HOH 17 2017 2017 HOH HOH B . F 3 HOH 18 2018 2018 HOH HOH B . F 3 HOH 19 2019 2019 HOH HOH B . F 3 HOH 20 2020 2020 HOH HOH B . F 3 HOH 21 2021 2021 HOH HOH B . F 3 HOH 22 2022 2022 HOH HOH B . F 3 HOH 23 2023 2023 HOH HOH B . F 3 HOH 24 2024 2024 HOH HOH B . F 3 HOH 25 2025 2025 HOH HOH B . F 3 HOH 26 2026 2026 HOH HOH B . F 3 HOH 27 2027 2027 HOH HOH B . F 3 HOH 28 2028 2028 HOH HOH B . F 3 HOH 29 2029 2029 HOH HOH B . F 3 HOH 30 2030 2030 HOH HOH B . F 3 HOH 31 2031 2031 HOH HOH B . F 3 HOH 32 2032 2032 HOH HOH B . F 3 HOH 33 2033 2033 HOH HOH B . F 3 HOH 34 2034 2034 HOH HOH B . F 3 HOH 35 2035 2035 HOH HOH B . F 3 HOH 36 2036 2036 HOH HOH B . F 3 HOH 37 2037 2037 HOH HOH B . F 3 HOH 38 2038 2038 HOH HOH B . F 3 HOH 39 2039 2039 HOH HOH B . F 3 HOH 40 2040 2040 HOH HOH B . F 3 HOH 41 2041 2041 HOH HOH B . F 3 HOH 42 2042 2042 HOH HOH B . F 3 HOH 43 2043 2043 HOH HOH B . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PQS monomeric 1 2 author_and_software_defined_assembly PQS monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,E 2 1 B,D,F # _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 NE2 ? A HIS 17 ? A HIS 17 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NA ? C HEM . ? A HEM 1117 ? 1_555 90.9 ? 2 NE2 ? A HIS 17 ? A HIS 17 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NB ? C HEM . ? A HEM 1117 ? 1_555 85.4 ? 3 NA ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NB ? C HEM . ? A HEM 1117 ? 1_555 89.6 ? 4 NE2 ? A HIS 17 ? A HIS 17 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NC ? C HEM . ? A HEM 1117 ? 1_555 91.6 ? 5 NA ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NC ? C HEM . ? A HEM 1117 ? 1_555 177.4 ? 6 NB ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 NC ? C HEM . ? A HEM 1117 ? 1_555 89.9 ? 7 NE2 ? A HIS 17 ? A HIS 17 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 ND ? C HEM . ? A HEM 1117 ? 1_555 90.3 ? 8 NA ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 ND ? C HEM . ? A HEM 1117 ? 1_555 90.1 ? 9 NB ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 ND ? C HEM . ? A HEM 1117 ? 1_555 175.7 ? 10 NC ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 ND ? C HEM . ? A HEM 1117 ? 1_555 90.6 ? 11 NE2 ? A HIS 17 ? A HIS 17 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 SD ? A MET 96 ? A MET 96 ? 1_555 178.9 ? 12 NA ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 SD ? A MET 96 ? A MET 96 ? 1_555 87.9 ? 13 NB ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 SD ? A MET 96 ? A MET 96 ? 1_555 94.4 ? 14 NC ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 SD ? A MET 96 ? A MET 96 ? 1_555 89.5 ? 15 ND ? C HEM . ? A HEM 1117 ? 1_555 FE ? C HEM . ? A HEM 1117 ? 1_555 SD ? A MET 96 ? A MET 96 ? 1_555 89.9 ? 16 NE2 ? B HIS 17 ? B HIS 17 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NA ? D HEM . ? B HEM 1117 ? 1_555 96.6 ? 17 NE2 ? B HIS 17 ? B HIS 17 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NB ? D HEM . ? B HEM 1117 ? 1_555 93.3 ? 18 NA ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NB ? D HEM . ? B HEM 1117 ? 1_555 89.5 ? 19 NE2 ? B HIS 17 ? B HIS 17 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NC ? D HEM . ? B HEM 1117 ? 1_555 83.8 ? 20 NA ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NC ? D HEM . ? B HEM 1117 ? 1_555 179.3 ? 21 NB ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 NC ? D HEM . ? B HEM 1117 ? 1_555 91.1 ? 22 NE2 ? B HIS 17 ? B HIS 17 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 ND ? D HEM . ? B HEM 1117 ? 1_555 87.2 ? 23 NA ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 ND ? D HEM . ? B HEM 1117 ? 1_555 91.8 ? 24 NB ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 ND ? D HEM . ? B HEM 1117 ? 1_555 178.5 ? 25 NC ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 ND ? D HEM . ? B HEM 1117 ? 1_555 87.5 ? 26 NE2 ? B HIS 17 ? B HIS 17 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 SD ? B MET 96 ? B MET 96 ? 1_555 175.6 ? 27 NA ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 SD ? B MET 96 ? B MET 96 ? 1_555 86.1 ? 28 NB ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 SD ? B MET 96 ? B MET 96 ? 1_555 90.2 ? 29 NC ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 SD ? B MET 96 ? B MET 96 ? 1_555 93.4 ? 30 ND ? D HEM . ? B HEM 1117 ? 1_555 FE ? D HEM . ? B HEM 1117 ? 1_555 SD ? B MET 96 ? B MET 96 ? 1_555 89.2 ? # 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 2004-06-17 2 'Structure model' 1 1 2012-06-20 3 'Structure model' 1 2 2018-06-13 # _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' 'Derived calculations' 3 2 'Structure model' 'Non-polymer description' 4 2 'Structure model' Other 5 2 'Structure model' 'Structure summary' 6 2 'Structure model' 'Version format compliance' 7 3 'Structure model' 'Data collection' 8 3 'Structure model' 'Structure summary' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category struct # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 3 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_struct.title' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement . ? 1 ? ? ? ? DENZO 'data reduction' . ? 2 ? ? ? ? SCALEPACK 'data scaling' . ? 3 ? ? ? ? AMoRE phasing . ? 4 ? ? ? ? # _pdbx_entry_details.entry_id 1VYD _pdbx_entry_details.compound_details 'ENGINEERED MUTATION GLY 116 GLU' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 2004 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2005 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.97 # 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 CD A ARG 43 ? ? NE A ARG 43 ? ? CZ A ARG 43 ? ? 133.07 123.60 9.47 1.40 N 2 1 NH1 A ARG 43 ? ? CZ A ARG 43 ? ? NH2 A ARG 43 ? ? 108.08 119.40 -11.32 1.10 N 3 1 NE A ARG 43 ? ? CZ A ARG 43 ? ? NH1 A ARG 43 ? ? 124.47 120.30 4.17 0.50 N 4 1 NE A ARG 43 ? ? CZ A ARG 43 ? ? NH2 A ARG 43 ? ? 127.44 120.30 7.14 0.50 N 5 1 CB A TYR 48 ? ? CG A TYR 48 ? ? CD2 A TYR 48 ? ? 116.46 121.00 -4.54 0.60 N 6 1 CB A TYR 53 ? ? CG A TYR 53 ? ? CD2 A TYR 53 ? ? 116.97 121.00 -4.03 0.60 N 7 1 CB A ASP 78 ? ? CG A ASP 78 ? ? OD1 A ASP 78 ? ? 112.49 118.30 -5.81 0.90 N 8 1 CB A ASP 78 ? ? CG A ASP 78 ? ? OD2 A ASP 78 ? ? 128.45 118.30 10.15 0.90 N 9 1 NE B ARG 43 ? ? CZ B ARG 43 ? ? NH2 B ARG 43 ? ? 112.69 120.30 -7.61 0.50 N 10 1 OE1 B GLU 50 ? ? CD B GLU 50 ? ? OE2 B GLU 50 ? ? 111.83 123.30 -11.47 1.20 N 11 1 CB B ASP 55 ? ? CG B ASP 55 ? ? OD2 B ASP 55 ? ? 129.82 118.30 11.52 0.90 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 ASP A 78 ? ? -166.21 87.75 2 1 PHE A 98 ? ? -170.85 132.53 3 1 ASP B 78 ? ? -172.40 85.05 # loop_ _pdbx_validate_main_chain_plane.id _pdbx_validate_main_chain_plane.PDB_model_num _pdbx_validate_main_chain_plane.auth_comp_id _pdbx_validate_main_chain_plane.auth_asym_id _pdbx_validate_main_chain_plane.auth_seq_id _pdbx_validate_main_chain_plane.PDB_ins_code _pdbx_validate_main_chain_plane.label_alt_id _pdbx_validate_main_chain_plane.improper_torsion_angle 1 1 LYS A 12 ? ? 17.48 2 1 GLY A 46 ? ? -10.25 3 1 TRP A 67 ? ? -11.65 4 1 CYS B 16 ? ? 11.32 5 1 ASP B 55 ? ? -12.08 6 1 ALA B 66 ? ? -10.24 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PROTOPORPHYRIN IX CONTAINING FE' HEM 3 water HOH #