data_5AGF # _entry.id 5AGF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.322 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5AGF PDBE EBI-62746 WWPDB D_1290062746 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 5AGF _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2015-01-30 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _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 'Gahfoor, D.D.' 1 'Kekilli, D.' 2 'Abdullah, G.H.' 3 'Dworkowski, F.S.N.' 4 'Hassan, H.G.' 5 'Wilson, M.T.' 6 'Hough, M.A.' 7 'Strange, R.W.' 8 # _citation.id primary _citation.title ;Hydrogen Bonding of the Dissociated Histidine Ligand is not Required for Formation of a Proximal No Adduct in Cytochrome C'. ; _citation.journal_abbrev J.Biol.Inorg.Chem. _citation.journal_volume 20 _citation.page_first 949 _citation.page_last ? _citation.year 2015 _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 26100643 _citation.pdbx_database_id_DOI 10.1007/S00775-015-1278-Y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ghafoor, D.D.' 1 ? primary 'Kekilli, D.' 2 ? primary 'Abdullah, G.H.' 3 ? primary 'Dworkowski, F.S.N.' 4 ? primary 'Hassan, H.G.' 5 ? primary 'Wilson, M.T.' 6 ? primary 'Strange, R.W.' 7 ? primary 'Hough, M.A.' 8 ? # _cell.entry_id 5AGF _cell.length_a 53.239 _cell.length_b 53.239 _cell.length_c 180.539 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AGF _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 # 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 C PRIME' 13644.483 1 ? YES ? ? 2 non-polymer syn 'HEME C' 618.503 1 ? ? ? ? 3 non-polymer syn 'NITRIC OXIDE' 30.006 1 ? ? ? ? 4 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 5 water nat water 18.015 194 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;(PCA)FAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDA ASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHQAYRKKK ; _entity_poly.pdbx_seq_one_letter_code_can ;QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFK QKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHQAYRKKK ; _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 PCA n 1 2 PHE n 1 3 ALA n 1 4 LYS n 1 5 PRO n 1 6 GLU n 1 7 ASP n 1 8 ALA n 1 9 VAL n 1 10 LYS n 1 11 TYR n 1 12 ARG n 1 13 GLN n 1 14 SER n 1 15 ALA n 1 16 LEU n 1 17 THR n 1 18 LEU n 1 19 MET n 1 20 ALA n 1 21 SER n 1 22 HIS n 1 23 PHE n 1 24 GLY n 1 25 ARG n 1 26 MET n 1 27 THR n 1 28 PRO n 1 29 VAL n 1 30 VAL n 1 31 LYS n 1 32 GLY n 1 33 GLN n 1 34 ALA n 1 35 PRO n 1 36 TYR n 1 37 ASP n 1 38 ALA n 1 39 ALA n 1 40 GLN n 1 41 ILE n 1 42 LYS n 1 43 ALA n 1 44 ASN n 1 45 VAL n 1 46 GLU n 1 47 VAL n 1 48 LEU n 1 49 LYS n 1 50 THR n 1 51 LEU n 1 52 SER n 1 53 ALA n 1 54 LEU n 1 55 PRO n 1 56 TRP n 1 57 ALA n 1 58 ALA n 1 59 PHE n 1 60 GLY n 1 61 PRO n 1 62 GLY n 1 63 THR n 1 64 GLU n 1 65 GLY n 1 66 GLY n 1 67 ASP n 1 68 ALA n 1 69 ARG n 1 70 PRO n 1 71 GLU n 1 72 ILE n 1 73 TRP n 1 74 SER n 1 75 ASP n 1 76 ALA n 1 77 ALA n 1 78 SER n 1 79 PHE n 1 80 LYS n 1 81 GLN n 1 82 LYS n 1 83 GLN n 1 84 GLN n 1 85 ALA n 1 86 PHE n 1 87 GLN n 1 88 ASP n 1 89 ASN n 1 90 ILE n 1 91 VAL n 1 92 LYS n 1 93 LEU n 1 94 SER n 1 95 ALA n 1 96 ALA n 1 97 ALA n 1 98 ASP n 1 99 ALA n 1 100 GLY n 1 101 ASP n 1 102 LEU n 1 103 ASP n 1 104 LYS n 1 105 LEU n 1 106 ARG n 1 107 ALA n 1 108 ALA n 1 109 PHE n 1 110 GLY n 1 111 ASP n 1 112 VAL n 1 113 GLY n 1 114 ALA n 1 115 SER n 1 116 CYS n 1 117 LYS n 1 118 ALA n 1 119 CYS n 1 120 HIS n 1 121 GLN n 1 122 ALA n 1 123 TYR n 1 124 ARG n 1 125 LYS n 1 126 LYS n 1 127 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 'ACHROMOBACTER XYLOSOXIDANS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 85698 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _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 CYCP_ALCXX _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P00138 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5AGF _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 127 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00138 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 127 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 127 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 5AGF _struct_ref_seq_dif.mon_id GLN _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 121 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P00138 _struct_ref_seq_dif.db_mon_id ASP _struct_ref_seq_dif.pdbx_seq_db_seq_num 121 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 121 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HEC non-polymer . 'HEME C' ? 'C34 H34 Fe N4 O4' 618.503 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 NO non-polymer . 'NITRIC OXIDE' 'Nitrogen monoxide' 'N O' 30.006 PCA 'L-peptide linking' n 'PYROGLUTAMIC ACID' ? 'C5 H7 N O3' 129.114 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 5AGF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.64 _exptl_crystal.density_percent_sol 53.4 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'AMMONIUM SULFATE, HEPES, pH 7.5' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2013-03-20 _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 'SI MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X10SA _diffrn_source.pdbx_wavelength 1.0 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5AGF _reflns.observed_criterion_sigma_I . _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 15.50 _reflns.d_resolution_high 1.09 _reflns.number_obs 62452 _reflns.number_all ? _reflns.percent_possible_obs 97.0 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.40 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.8 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.09 _reflns_shell.d_res_low 1.13 _reflns_shell.percent_possible_all 76.0 _reflns_shell.Rmerge_I_obs 0.73 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.20 _reflns_shell.pdbx_redundancy 4.8 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5AGF _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 59145 _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 46.11 _refine.ls_d_res_high 1.09 _refine.ls_percent_reflns_obs 96.94 _refine.ls_R_factor_obs 0.17029 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.16950 _refine.ls_R_factor_R_free 0.18521 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 3155 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.973 _refine.correlation_coeff_Fo_to_Fc_free 0.969 _refine.B_iso_mean 16.480 _refine.aniso_B[1][1] -0.39 _refine.aniso_B[2][2] -0.39 _refine.aniso_B[3][3] 1.28 _refine.aniso_B[1][2] -0.20 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct OTHER _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.032 _refine.pdbx_overall_ESU_R_Free 0.031 _refine.overall_SU_ML 0.028 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.351 _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 941 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 50 _refine_hist.number_atoms_solvent 194 _refine_hist.number_atoms_total 1185 _refine_hist.d_res_high 1.09 _refine_hist.d_res_low 46.11 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.016 0.020 ? 1156 'X-RAY DIFFRACTION' ? r_bond_other_d 0.003 0.020 ? 1062 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.270 2.040 ? 1594 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.801 3.000 ? 2463 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.839 5.000 ? 157 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.038 25.208 ? 48 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 13.895 15.000 ? 181 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 20.558 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.105 0.200 ? 160 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.011 0.021 ? 1429 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.008 0.020 ? 257 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 3.626 1.515 ? 571 'X-RAY DIFFRACTION' ? r_mcbond_other 3.626 1.513 ? 569 'X-RAY DIFFRACTION' ? r_mcangle_it 4.815 2.308 ? 722 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.259 1.606 ? 585 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 4.289 3.000 ? 2218 'X-RAY DIFFRACTION' ? r_sphericity_free 70.497 5.000 ? 23 'X-RAY DIFFRACTION' ? r_sphericity_bonded 15.874 5.000 ? 2355 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.090 _refine_ls_shell.d_res_low 1.118 _refine_ls_shell.number_reflns_R_work 3163 _refine_ls_shell.R_factor_R_work 0.295 _refine_ls_shell.percent_reflns_obs 71.66 _refine_ls_shell.R_factor_R_free 0.277 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 145 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 5AGF _struct.title 'Nitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans' _struct.pdbx_descriptor 'CYTOCHROME C PRIME' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5AGF _struct_keywords.pdbx_keywords OXIDOREDUCTASE _struct_keywords.text 'OXIDOREDUCTASE, PROXIMAL NO, CYTOCHROME, GAS SENSING, NITRIC OXIDE' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 4 ? ARG A 25 ? LYS A 4 ARG A 25 1 ? 22 HELX_P HELX_P2 2 MET A 26 ? LYS A 31 ? MET A 26 LYS A 31 1 ? 6 HELX_P HELX_P3 3 ASP A 37 ? ALA A 53 ? ASP A 37 ALA A 53 1 ? 17 HELX_P HELX_P4 4 LEU A 54 ? PHE A 59 ? LEU A 54 PHE A 59 5 ? 6 HELX_P HELX_P5 5 PRO A 70 ? ASP A 75 ? PRO A 70 ASP A 75 1 ? 6 HELX_P HELX_P6 6 ASP A 75 ? GLY A 100 ? ASP A 75 GLY A 100 1 ? 26 HELX_P HELX_P7 7 ASP A 101 ? ARG A 124 ? ASP A 101 ARG A 124 1 ? 24 # _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 covale1 covale both ? A PCA 1 C ? ? ? 1_555 A PHE 2 N ? ? A PCA 1 A PHE 2 1_555 ? ? ? ? ? ? ? 1.342 ? metalc1 metalc ? ? B HEC . FE ? ? ? 1_555 C NO . N ? ? A HEC 128 A NO 129 1_555 ? ? ? ? ? ? ? 1.790 ? covale2 covale none ? B HEC . CAC ? ? ? 1_555 A CYS 119 SG A ? A HEC 128 A CYS 119 1_555 ? ? ? ? ? ? ? 1.928 ? metalc2 metalc ? ? B HEC . FE ? ? ? 1_555 C NO . O ? ? A HEC 128 A NO 129 1_555 ? ? ? ? ? ? ? 2.713 ? covale3 covale none ? B HEC . CAB ? ? ? 1_555 A CYS 116 SG ? ? A HEC 128 A CYS 116 1_555 ? ? ? ? ? ? ? 1.964 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # 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 HEC A 128' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE NO A 129' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE SO4 A 130' # 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 ARG A 12 ? ARG A 12 . ? 1_555 ? 2 AC1 21 GLN A 13 ? GLN A 13 . ? 1_555 ? 3 AC1 21 LEU A 16 ? LEU A 16 . ? 1_555 ? 4 AC1 21 THR A 17 ? THR A 17 . ? 1_555 ? 5 AC1 21 MET A 19 ? MET A 19 . ? 1_555 ? 6 AC1 21 TRP A 56 ? TRP A 56 . ? 1_555 ? 7 AC1 21 PHE A 59 ? PHE A 59 . ? 1_555 ? 8 AC1 21 GLY A 65 ? GLY A 65 . ? 1_555 ? 9 AC1 21 ASP A 67 ? ASP A 67 . ? 1_555 ? 10 AC1 21 ILE A 72 ? ILE A 72 . ? 1_555 ? 11 AC1 21 PHE A 79 ? PHE A 79 . ? 1_555 ? 12 AC1 21 GLN A 83 ? GLN A 83 . ? 1_555 ? 13 AC1 21 PHE A 86 ? PHE A 86 . ? 1_555 ? 14 AC1 21 CYS A 116 ? CYS A 116 . ? 1_555 ? 15 AC1 21 CYS A 119 ? CYS A 119 . ? 1_555 ? 16 AC1 21 TYR A 123 ? TYR A 123 . ? 1_555 ? 17 AC1 21 ARG A 124 ? ARG A 124 . ? 1_555 ? 18 AC1 21 NO C . ? NO A 129 . ? 1_555 ? 19 AC1 21 SO4 D . ? SO4 A 130 . ? 1_555 ? 20 AC1 21 HOH E . ? HOH A 2060 . ? 1_555 ? 21 AC1 21 HOH E . ? HOH A 2145 . ? 1_555 ? 22 AC2 3 HIS A 120 ? HIS A 120 . ? 1_555 ? 23 AC2 3 ARG A 124 ? ARG A 124 . ? 1_555 ? 24 AC2 3 HEC B . ? HEC A 128 . ? 1_555 ? 25 AC3 5 ARG A 124 ? ARG A 124 . ? 1_555 ? 26 AC3 5 HEC B . ? HEC A 128 . ? 1_555 ? 27 AC3 5 HOH E . ? HOH A 2196 . ? 1_555 ? 28 AC3 5 HOH E . ? HOH A 2197 . ? 1_555 ? 29 AC3 5 HOH E . ? HOH A 2198 . ? 1_555 ? # _database_PDB_matrix.entry_id 5AGF _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 5AGF _atom_sites.fract_transf_matrix[1][1] 0.018783 _atom_sites.fract_transf_matrix[1][2] 0.010844 _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] 0.021689 _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] 0.005539 _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 PCA 1 1 1 PCA PCA A . n A 1 2 PHE 2 2 2 PHE PHE A . n A 1 3 ALA 3 3 3 ALA ALA A . n A 1 4 LYS 4 4 4 LYS LYS A . n A 1 5 PRO 5 5 5 PRO PRO A . n A 1 6 GLU 6 6 6 GLU GLU A . n A 1 7 ASP 7 7 7 ASP ASP A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 VAL 9 9 9 VAL VAL A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 TYR 11 11 11 TYR TYR A . n A 1 12 ARG 12 12 12 ARG ARG A . n A 1 13 GLN 13 13 13 GLN GLN A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 ALA 15 15 15 ALA ALA A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 THR 17 17 17 THR THR A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 MET 19 19 19 MET MET A . n A 1 20 ALA 20 20 20 ALA ALA A . n A 1 21 SER 21 21 21 SER SER A . n A 1 22 HIS 22 22 22 HIS HIS A . n A 1 23 PHE 23 23 23 PHE PHE A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 ARG 25 25 25 ARG ARG A . n A 1 26 MET 26 26 26 MET MET A . n A 1 27 THR 27 27 27 THR THR A . n A 1 28 PRO 28 28 28 PRO PRO A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 VAL 30 30 30 VAL VAL A . n A 1 31 LYS 31 31 31 LYS LYS A . n A 1 32 GLY 32 32 32 GLY GLY A . n A 1 33 GLN 33 33 33 GLN GLN A . n A 1 34 ALA 34 34 34 ALA ALA A . n A 1 35 PRO 35 35 35 PRO PRO A . n A 1 36 TYR 36 36 36 TYR TYR A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 ALA 38 38 38 ALA ALA A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 GLN 40 40 40 GLN GLN A . n A 1 41 ILE 41 41 41 ILE ILE A . n A 1 42 LYS 42 42 42 LYS LYS A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 ASN 44 44 44 ASN ASN A . n A 1 45 VAL 45 45 45 VAL VAL A . n A 1 46 GLU 46 46 46 GLU GLU A . n A 1 47 VAL 47 47 47 VAL VAL A . n A 1 48 LEU 48 48 48 LEU LEU A . n A 1 49 LYS 49 49 49 LYS LYS A . n A 1 50 THR 50 50 50 THR THR A . n A 1 51 LEU 51 51 51 LEU LEU A . n A 1 52 SER 52 52 52 SER SER A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 LEU 54 54 54 LEU LEU A . n A 1 55 PRO 55 55 55 PRO PRO A . n A 1 56 TRP 56 56 56 TRP TRP A . n A 1 57 ALA 57 57 57 ALA ALA A . n A 1 58 ALA 58 58 58 ALA ALA A . n A 1 59 PHE 59 59 59 PHE PHE A . n A 1 60 GLY 60 60 60 GLY GLY A . n A 1 61 PRO 61 61 61 PRO PRO A . n A 1 62 GLY 62 62 62 GLY GLY A . n A 1 63 THR 63 63 63 THR THR A . n A 1 64 GLU 64 64 64 GLU GLU A . n A 1 65 GLY 65 65 65 GLY GLY A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 ASP 67 67 67 ASP ASP A . n A 1 68 ALA 68 68 68 ALA ALA A . n A 1 69 ARG 69 69 69 ARG ARG A . n A 1 70 PRO 70 70 70 PRO PRO A . n A 1 71 GLU 71 71 71 GLU GLU A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 TRP 73 73 73 TRP TRP A . n A 1 74 SER 74 74 74 SER SER A . n A 1 75 ASP 75 75 75 ASP ASP A . n A 1 76 ALA 76 76 76 ALA ALA A . n A 1 77 ALA 77 77 77 ALA ALA A . n A 1 78 SER 78 78 78 SER SER A . n A 1 79 PHE 79 79 79 PHE PHE A . n A 1 80 LYS 80 80 80 LYS LYS A . n A 1 81 GLN 81 81 81 GLN GLN A . n A 1 82 LYS 82 82 82 LYS LYS A . n A 1 83 GLN 83 83 83 GLN GLN A . n A 1 84 GLN 84 84 84 GLN GLN A . n A 1 85 ALA 85 85 85 ALA ALA A . n A 1 86 PHE 86 86 86 PHE PHE A . n A 1 87 GLN 87 87 87 GLN GLN A . n A 1 88 ASP 88 88 88 ASP ASP A . n A 1 89 ASN 89 89 89 ASN ASN A . n A 1 90 ILE 90 90 90 ILE ILE A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 LYS 92 92 92 LYS LYS A . n A 1 93 LEU 93 93 93 LEU LEU A . n A 1 94 SER 94 94 94 SER SER A . n A 1 95 ALA 95 95 95 ALA ALA A . n A 1 96 ALA 96 96 96 ALA ALA A . n A 1 97 ALA 97 97 97 ALA ALA A . n A 1 98 ASP 98 98 98 ASP ASP A . n A 1 99 ALA 99 99 99 ALA ALA A . n A 1 100 GLY 100 100 100 GLY GLY A . n A 1 101 ASP 101 101 101 ASP ASP A . n A 1 102 LEU 102 102 102 LEU LEU A . n A 1 103 ASP 103 103 103 ASP ASP A . n A 1 104 LYS 104 104 104 LYS LYS A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 ARG 106 106 106 ARG ARG A . n A 1 107 ALA 107 107 107 ALA ALA A . n A 1 108 ALA 108 108 108 ALA ALA A . n A 1 109 PHE 109 109 109 PHE PHE A . n A 1 110 GLY 110 110 110 GLY GLY A . n A 1 111 ASP 111 111 111 ASP ASP A . n A 1 112 VAL 112 112 112 VAL VAL A . n A 1 113 GLY 113 113 113 GLY GLY A . n A 1 114 ALA 114 114 114 ALA ALA A . n A 1 115 SER 115 115 115 SER SER A . n A 1 116 CYS 116 116 116 CYS CYS A . n A 1 117 LYS 117 117 117 LYS LYS A . n A 1 118 ALA 118 118 118 ALA ALA A . n A 1 119 CYS 119 119 119 CYS CYS A . n A 1 120 HIS 120 120 120 HIS HIS A . n A 1 121 GLN 121 121 121 GLN GLN A . n A 1 122 ALA 122 122 122 ALA ALA A . n A 1 123 TYR 123 123 123 TYR TYR A . n A 1 124 ARG 124 124 124 ARG ARG A . n A 1 125 LYS 125 125 125 LYS LYS A . n A 1 126 LYS 126 126 ? ? ? A . n A 1 127 LYS 127 127 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HEC 1 128 128 HEC HEC A . C 3 NO 1 129 129 NO NO A . D 4 SO4 1 130 130 SO4 SO4 A . E 5 HOH 1 2001 2001 HOH HOH A . E 5 HOH 2 2002 2002 HOH HOH A . E 5 HOH 3 2003 2003 HOH HOH A . E 5 HOH 4 2004 2004 HOH HOH A . E 5 HOH 5 2005 2005 HOH HOH A . E 5 HOH 6 2006 2006 HOH HOH A . E 5 HOH 7 2007 2007 HOH HOH A . E 5 HOH 8 2008 2008 HOH HOH A . E 5 HOH 9 2009 2009 HOH HOH A . E 5 HOH 10 2010 2010 HOH HOH A . E 5 HOH 11 2011 2011 HOH HOH A . E 5 HOH 12 2012 2012 HOH HOH A . E 5 HOH 13 2013 2013 HOH HOH A . E 5 HOH 14 2014 2014 HOH HOH A . E 5 HOH 15 2015 2015 HOH HOH A . E 5 HOH 16 2016 2016 HOH HOH A . E 5 HOH 17 2017 2017 HOH HOH A . E 5 HOH 18 2018 2018 HOH HOH A . E 5 HOH 19 2019 2019 HOH HOH A . E 5 HOH 20 2020 2020 HOH HOH A . E 5 HOH 21 2021 2021 HOH HOH A . E 5 HOH 22 2022 2022 HOH HOH A . E 5 HOH 23 2023 2023 HOH HOH A . E 5 HOH 24 2024 2024 HOH HOH A . E 5 HOH 25 2025 2025 HOH HOH A . E 5 HOH 26 2026 2026 HOH HOH A . E 5 HOH 27 2027 2027 HOH HOH A . E 5 HOH 28 2028 2028 HOH HOH A . E 5 HOH 29 2029 2029 HOH HOH A . E 5 HOH 30 2030 2030 HOH HOH A . E 5 HOH 31 2031 2031 HOH HOH A . E 5 HOH 32 2032 2032 HOH HOH A . E 5 HOH 33 2033 2033 HOH HOH A . E 5 HOH 34 2034 2034 HOH HOH A . E 5 HOH 35 2035 2035 HOH HOH A . E 5 HOH 36 2036 2036 HOH HOH A . E 5 HOH 37 2037 2037 HOH HOH A . E 5 HOH 38 2038 2038 HOH HOH A . E 5 HOH 39 2039 2039 HOH HOH A . E 5 HOH 40 2040 2040 HOH HOH A . E 5 HOH 41 2041 2041 HOH HOH A . E 5 HOH 42 2042 2042 HOH HOH A . E 5 HOH 43 2043 2043 HOH HOH A . E 5 HOH 44 2044 2044 HOH HOH A . E 5 HOH 45 2045 2045 HOH HOH A . E 5 HOH 46 2046 2046 HOH HOH A . E 5 HOH 47 2047 2047 HOH HOH A . E 5 HOH 48 2048 2048 HOH HOH A . E 5 HOH 49 2049 2049 HOH HOH A . E 5 HOH 50 2050 2050 HOH HOH A . E 5 HOH 51 2051 2051 HOH HOH A . E 5 HOH 52 2052 2052 HOH HOH A . E 5 HOH 53 2053 2053 HOH HOH A . E 5 HOH 54 2054 2054 HOH HOH A . E 5 HOH 55 2055 2055 HOH HOH A . E 5 HOH 56 2056 2056 HOH HOH A . E 5 HOH 57 2057 2057 HOH HOH A . E 5 HOH 58 2058 2058 HOH HOH A . E 5 HOH 59 2059 2059 HOH HOH A . E 5 HOH 60 2060 2060 HOH HOH A . E 5 HOH 61 2061 2061 HOH HOH A . E 5 HOH 62 2062 2062 HOH HOH A . E 5 HOH 63 2063 2063 HOH HOH A . E 5 HOH 64 2064 2064 HOH HOH A . E 5 HOH 65 2065 2065 HOH HOH A . E 5 HOH 66 2066 2066 HOH HOH A . E 5 HOH 67 2067 2067 HOH HOH A . E 5 HOH 68 2068 2068 HOH HOH A . E 5 HOH 69 2069 2069 HOH HOH A . E 5 HOH 70 2070 2070 HOH HOH A . E 5 HOH 71 2071 2071 HOH HOH A . E 5 HOH 72 2072 2072 HOH HOH A . E 5 HOH 73 2073 2073 HOH HOH A . E 5 HOH 74 2074 2074 HOH HOH A . E 5 HOH 75 2075 2075 HOH HOH A . E 5 HOH 76 2076 2076 HOH HOH A . E 5 HOH 77 2077 2077 HOH HOH A . E 5 HOH 78 2078 2078 HOH HOH A . E 5 HOH 79 2079 2079 HOH HOH A . E 5 HOH 80 2080 2080 HOH HOH A . E 5 HOH 81 2081 2081 HOH HOH A . E 5 HOH 82 2082 2082 HOH HOH A . E 5 HOH 83 2083 2083 HOH HOH A . E 5 HOH 84 2084 2084 HOH HOH A . E 5 HOH 85 2085 2085 HOH HOH A . E 5 HOH 86 2086 2086 HOH HOH A . E 5 HOH 87 2087 2087 HOH HOH A . E 5 HOH 88 2088 2088 HOH HOH A . E 5 HOH 89 2089 2089 HOH HOH A . E 5 HOH 90 2090 2090 HOH HOH A . E 5 HOH 91 2091 2091 HOH HOH A . E 5 HOH 92 2092 2092 HOH HOH A . E 5 HOH 93 2093 2093 HOH HOH A . E 5 HOH 94 2094 2094 HOH HOH A . E 5 HOH 95 2095 2095 HOH HOH A . E 5 HOH 96 2096 2096 HOH HOH A . E 5 HOH 97 2097 2097 HOH HOH A . E 5 HOH 98 2098 2098 HOH HOH A . E 5 HOH 99 2099 2099 HOH HOH A . E 5 HOH 100 2100 2100 HOH HOH A . E 5 HOH 101 2101 2101 HOH HOH A . E 5 HOH 102 2102 2102 HOH HOH A . E 5 HOH 103 2103 2103 HOH HOH A . E 5 HOH 104 2104 2104 HOH HOH A . E 5 HOH 105 2105 2105 HOH HOH A . E 5 HOH 106 2106 2106 HOH HOH A . E 5 HOH 107 2107 2107 HOH HOH A . E 5 HOH 108 2108 2108 HOH HOH A . E 5 HOH 109 2109 2109 HOH HOH A . E 5 HOH 110 2110 2110 HOH HOH A . E 5 HOH 111 2111 2111 HOH HOH A . E 5 HOH 112 2112 2112 HOH HOH A . E 5 HOH 113 2113 2113 HOH HOH A . E 5 HOH 114 2114 2114 HOH HOH A . E 5 HOH 115 2115 2115 HOH HOH A . E 5 HOH 116 2116 2116 HOH HOH A . E 5 HOH 117 2117 2117 HOH HOH A . E 5 HOH 118 2119 2119 HOH HOH A . E 5 HOH 119 2120 2120 HOH HOH A . E 5 HOH 120 2121 2121 HOH HOH A . E 5 HOH 121 2122 2122 HOH HOH A . E 5 HOH 122 2123 2123 HOH HOH A . E 5 HOH 123 2124 2124 HOH HOH A . E 5 HOH 124 2125 2125 HOH HOH A . E 5 HOH 125 2126 2126 HOH HOH A . E 5 HOH 126 2127 2127 HOH HOH A . E 5 HOH 127 2128 2128 HOH HOH A . E 5 HOH 128 2129 2129 HOH HOH A . E 5 HOH 129 2130 2130 HOH HOH A . E 5 HOH 130 2131 2131 HOH HOH A . E 5 HOH 131 2132 2132 HOH HOH A . E 5 HOH 132 2133 2133 HOH HOH A . E 5 HOH 133 2134 2134 HOH HOH A . E 5 HOH 134 2135 2135 HOH HOH A . E 5 HOH 135 2136 2136 HOH HOH A . E 5 HOH 136 2137 2137 HOH HOH A . E 5 HOH 137 2138 2138 HOH HOH A . E 5 HOH 138 2139 2139 HOH HOH A . E 5 HOH 139 2140 2140 HOH HOH A . E 5 HOH 140 2141 2141 HOH HOH A . E 5 HOH 141 2142 2142 HOH HOH A . E 5 HOH 142 2143 2143 HOH HOH A . E 5 HOH 143 2144 2144 HOH HOH A . E 5 HOH 144 2145 2145 HOH HOH A . E 5 HOH 145 2146 2146 HOH HOH A . E 5 HOH 146 2147 2147 HOH HOH A . E 5 HOH 147 2148 2148 HOH HOH A . E 5 HOH 148 2149 2149 HOH HOH A . E 5 HOH 149 2151 2151 HOH HOH A . E 5 HOH 150 2152 2152 HOH HOH A . E 5 HOH 151 2153 2153 HOH HOH A . E 5 HOH 152 2154 2154 HOH HOH A . E 5 HOH 153 2156 2156 HOH HOH A . E 5 HOH 154 2157 2157 HOH HOH A . E 5 HOH 155 2158 2158 HOH HOH A . E 5 HOH 156 2159 2159 HOH HOH A . E 5 HOH 157 2160 2160 HOH HOH A . E 5 HOH 158 2161 2161 HOH HOH A . E 5 HOH 159 2162 2162 HOH HOH A . E 5 HOH 160 2163 2163 HOH HOH A . E 5 HOH 161 2164 2164 HOH HOH A . E 5 HOH 162 2165 2165 HOH HOH A . E 5 HOH 163 2166 2166 HOH HOH A . E 5 HOH 164 2168 2168 HOH HOH A . E 5 HOH 165 2169 2169 HOH HOH A . E 5 HOH 166 2170 2170 HOH HOH A . E 5 HOH 167 2171 2171 HOH HOH A . E 5 HOH 168 2172 2172 HOH HOH A . E 5 HOH 169 2173 2173 HOH HOH A . E 5 HOH 170 2174 2174 HOH HOH A . E 5 HOH 171 2175 2175 HOH HOH A . E 5 HOH 172 2176 2176 HOH HOH A . E 5 HOH 173 2177 2177 HOH HOH A . E 5 HOH 174 2178 2178 HOH HOH A . E 5 HOH 175 2179 2179 HOH HOH A . E 5 HOH 176 2180 2180 HOH HOH A . E 5 HOH 177 2181 2181 HOH HOH A . E 5 HOH 178 2182 2182 HOH HOH A . E 5 HOH 179 2183 2183 HOH HOH A . E 5 HOH 180 2184 2184 HOH HOH A . E 5 HOH 181 2185 2185 HOH HOH A . E 5 HOH 182 2186 2186 HOH HOH A . E 5 HOH 183 2187 2187 HOH HOH A . E 5 HOH 184 2188 2188 HOH HOH A . E 5 HOH 185 2189 2189 HOH HOH A . E 5 HOH 186 2190 2190 HOH HOH A . E 5 HOH 187 2191 2191 HOH HOH A . E 5 HOH 188 2192 2192 HOH HOH A . E 5 HOH 189 2193 2193 HOH HOH A . E 5 HOH 190 2194 2194 HOH HOH A . E 5 HOH 191 2195 2195 HOH HOH A . E 5 HOH 192 2196 2196 HOH HOH A . E 5 HOH 193 2197 2197 HOH HOH A . E 5 HOH 194 2198 2198 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id PCA _pdbx_struct_mod_residue.label_seq_id 1 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id PCA _pdbx_struct_mod_residue.auth_seq_id 1 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id GLU _pdbx_struct_mod_residue.details 'PYROGLUTAMIC ACID' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1460 ? 1 MORE -28.6 ? 1 'SSA (A^2)' 12780 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 10_555 -y,-x,-z+1/6 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 30.0898333333 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 2039 ? E HOH . 2 1 A HOH 2057 ? E HOH . # 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 N ? C NO . ? A NO 129 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NA ? B HEC . ? A HEC 128 ? 1_555 100.1 ? 2 N ? C NO . ? A NO 129 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NB ? B HEC . ? A HEC 128 ? 1_555 97.7 ? 3 NA ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NB ? B HEC . ? A HEC 128 ? 1_555 89.3 ? 4 N ? C NO . ? A NO 129 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NC ? B HEC . ? A HEC 128 ? 1_555 95.4 ? 5 NA ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NC ? B HEC . ? A HEC 128 ? 1_555 164.5 ? 6 NB ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 NC ? B HEC . ? A HEC 128 ? 1_555 89.6 ? 7 N ? C NO . ? A NO 129 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 ND ? B HEC . ? A HEC 128 ? 1_555 94.8 ? 8 NA ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 ND ? B HEC . ? A HEC 128 ? 1_555 88.0 ? 9 NB ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 ND ? B HEC . ? A HEC 128 ? 1_555 167.5 ? 10 NC ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 ND ? B HEC . ? A HEC 128 ? 1_555 89.7 ? 11 N ? C NO . ? A NO 129 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 O ? C NO . ? A NO 129 ? 1_555 19.4 ? 12 NA ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 O ? C NO . ? A NO 129 ? 1_555 113.0 ? 13 NB ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 O ? C NO . ? A NO 129 ? 1_555 111.2 ? 14 NC ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 O ? C NO . ? A NO 129 ? 1_555 81.8 ? 15 ND ? B HEC . ? A HEC 128 ? 1_555 FE ? B HEC . ? A HEC 128 ? 1_555 O ? C NO . ? A NO 129 ? 1_555 81.1 ? # 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 2015-09-09 2 'Structure model' 1 1 2015-11-25 3 'Structure model' 1 2 2016-12-07 4 'Structure model' 2 0 2020-03-11 # _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' 'Atomic model' 2 2 'Structure model' Other 3 3 'Structure model' 'Atomic model' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Non-polymer description' 6 3 'Structure model' Other 7 4 'Structure model' Advisory 8 4 'Structure model' 'Derived calculations' 9 4 'Structure model' Other 10 4 'Structure model' 'Polymer sequence' # 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' entity_poly 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 4 4 'Structure model' struct_conn # 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' '_entity_poly.pdbx_seq_one_letter_code_can' 2 4 'Structure model' '_pdbx_database_status.status_code_sf' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.8.0103 ? 1 HKL-2000 'data reduction' . ? 2 HKL-2000 'data scaling' . ? 3 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OG _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 SER _pdbx_validate_close_contact.auth_seq_id_1 74 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 B _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2146 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.90 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 NE2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLN _pdbx_validate_symm_contact.auth_seq_id_1 81 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 2023 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 8_665 _pdbx_validate_symm_contact.dist 2.13 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 NE A ARG 69 ? ? CZ A ARG 69 ? ? 1.209 1.326 -0.117 0.013 N 2 1 CB A SER 74 ? A OG A SER 74 ? A 1.507 1.418 0.089 0.013 N 3 1 CB A SER 74 ? B OG A SER 74 ? B 1.519 1.418 0.101 0.013 N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 75 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id A _pdbx_validate_torsion.phi -112.55 _pdbx_validate_torsion.psi 59.49 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 2007 ? 5.89 . 2 1 O ? A HOH 2047 ? 6.33 . 3 1 O ? A HOH 2048 ? 6.58 . 4 1 O ? A HOH 2067 ? 5.94 . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A LYS 126 ? A LYS 126 2 1 Y 1 A LYS 127 ? A LYS 127 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'HEME C' HEC 3 'NITRIC OXIDE' NO 4 'SULFATE ION' SO4 5 water HOH #