data_3DP5 # _entry.id 3DP5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.315 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3DP5 RCSB RCSB048315 WWPDB D_1000048315 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3DP5 _pdbx_database_status.recvd_initial_deposition_date 2008-07-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lukat, P.' 1 'Hoffmann, M.' 2 'Einsle, O.' 3 # _citation.id primary _citation.title 'Crystal packing of the c(6)-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II' _citation.journal_abbrev 'ACTA CRYSTALLOGR.,SECT.D' _citation.journal_volume 64 _citation.page_first 919 _citation.page_last 926 _citation.year 2008 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18703839 _citation.pdbx_database_id_DOI 10.1107/S0907444908021306 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lukat, P.' 1 ? primary 'Hoffmann, M.' 2 ? primary 'Einsle, O.' 3 ? # _cell.entry_id 3DP5 _cell.length_a 53.475 _cell.length_b 40.125 _cell.length_c 42.085 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3DP5 _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? # 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 family protein' 10351.609 1 ? ? 'UNP residues 26-104, OmcF' ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 non-polymer syn 'HEME C' 618.503 1 ? ? ? ? 4 water nat water 18.015 117 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name OmcF # _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 ;AASWSHPQFEKGAETAVPNSGGGELFATHCAGCHPQGGNTVHPEKTLARARREANGIRTVRDVAAYIRNPGPGMPAFGEA MIPPADALKIGEYVVASFP ; _entity_poly.pdbx_seq_one_letter_code_can ;AASWSHPQFEKGAETAVPNSGGGELFATHCAGCHPQGGNTVHPEKTLARARREANGIRTVRDVAAYIRNPGPGMPAFGEA MIPPADALKIGEYVVASFP ; _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 ALA n 1 2 ALA n 1 3 SER n 1 4 TRP n 1 5 SER n 1 6 HIS n 1 7 PRO n 1 8 GLN n 1 9 PHE n 1 10 GLU n 1 11 LYS n 1 12 GLY n 1 13 ALA n 1 14 GLU n 1 15 THR n 1 16 ALA n 1 17 VAL n 1 18 PRO n 1 19 ASN n 1 20 SER n 1 21 GLY n 1 22 GLY n 1 23 GLY n 1 24 GLU n 1 25 LEU n 1 26 PHE n 1 27 ALA n 1 28 THR n 1 29 HIS n 1 30 CYS n 1 31 ALA n 1 32 GLY n 1 33 CYS n 1 34 HIS n 1 35 PRO n 1 36 GLN n 1 37 GLY n 1 38 GLY n 1 39 ASN n 1 40 THR n 1 41 VAL n 1 42 HIS n 1 43 PRO n 1 44 GLU n 1 45 LYS n 1 46 THR n 1 47 LEU n 1 48 ALA n 1 49 ARG n 1 50 ALA n 1 51 ARG n 1 52 ARG n 1 53 GLU n 1 54 ALA n 1 55 ASN n 1 56 GLY n 1 57 ILE n 1 58 ARG n 1 59 THR n 1 60 VAL n 1 61 ARG n 1 62 ASP n 1 63 VAL n 1 64 ALA n 1 65 ALA n 1 66 TYR n 1 67 ILE n 1 68 ARG n 1 69 ASN n 1 70 PRO n 1 71 GLY n 1 72 PRO n 1 73 GLY n 1 74 MET n 1 75 PRO n 1 76 ALA n 1 77 PHE n 1 78 GLY n 1 79 GLU n 1 80 ALA n 1 81 MET n 1 82 ILE n 1 83 PRO n 1 84 PRO n 1 85 ALA n 1 86 ASP n 1 87 ALA n 1 88 LEU n 1 89 LYS n 1 90 ILE n 1 91 GLY n 1 92 GLU n 1 93 TYR n 1 94 VAL n 1 95 VAL n 1 96 ALA n 1 97 SER n 1 98 PHE n 1 99 PRO 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 GSU2432 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain PCA _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details 'Coexpression with the CCM-system on pEC86 plasmid' _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Geobacter sulfurreducens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 35554 _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 'Bl21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name 'pET22b(+)' _entity_src_gen.plasmid_details 'Modified with N-terminal Strep-tag II' _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q74AE4_GEOSL _struct_ref.pdbx_db_accession Q74AE4 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GGGELFATHCAGCHPQGGNTVHPEKTLARARREANGIRTVRDVAAYIRNPGPGMPAFGEAMIPPADALKIGEYVVASFP _struct_ref.pdbx_align_begin 26 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DP5 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 21 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 99 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q74AE4 _struct_ref_seq.db_align_beg 26 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 104 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 26 _struct_ref_seq.pdbx_auth_seq_align_end 104 # 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 3DP5 ALA A 1 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -20 1 1 3DP5 ALA A 2 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -19 2 1 3DP5 SER A 3 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -18 3 1 3DP5 TRP A 4 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -17 4 1 3DP5 SER A 5 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -16 5 1 3DP5 HIS A 6 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -15 6 1 3DP5 PRO A 7 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -14 7 1 3DP5 GLN A 8 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -13 8 1 3DP5 PHE A 9 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -12 9 1 3DP5 GLU A 10 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -11 10 1 3DP5 LYS A 11 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -10 11 1 3DP5 GLY A 12 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -9 12 1 3DP5 ALA A 13 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -8 13 1 3DP5 GLU A 14 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -7 14 1 3DP5 THR A 15 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -6 15 1 3DP5 ALA A 16 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -5 16 1 3DP5 VAL A 17 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -4 17 1 3DP5 PRO A 18 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -3 18 1 3DP5 ASN A 19 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -2 19 1 3DP5 SER A 20 ? UNP Q74AE4 ? ? 'EXPRESSION TAG' -1 20 # 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 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 3DP5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.60 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details '1.4-1.8M ammonium sulfate, 2% PEG400, 100mM HEPES/NaOH, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2007-02-15 _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 'Osmic Blue' _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 'RIGAKU MICROMAX-007' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3DP5 _reflns.observed_criterion_sigma_F 2.0 _reflns.observed_criterion_sigma_I 2.0 _reflns.d_resolution_high 1.86 _reflns.d_resolution_low 33.08 _reflns.number_all ? _reflns.number_obs 8066 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.1050 _reflns.pdbx_netI_over_sigmaI 23.50 _reflns.B_iso_Wilson_estimate 21.934 _reflns.pdbx_redundancy 21.78 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.86 _reflns_shell.d_res_low 1.96 _reflns_shell.percent_possible_all 98.5 _reflns_shell.Rmerge_I_obs 0.4952 _reflns_shell.pdbx_Rsym_value 0.4952 _reflns_shell.meanI_over_sigI_obs 6.060 _reflns_shell.pdbx_redundancy 16.04 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 394 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3DP5 _refine.ls_number_reflns_obs 7669 _refine.ls_number_reflns_all 7684 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.08 _refine.ls_d_res_high 1.86 _refine.ls_percent_reflns_obs 99.68 _refine.ls_R_factor_obs 0.17236 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.17045 _refine.ls_R_factor_R_free 0.20987 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 371 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.959 _refine.correlation_coeff_Fo_to_Fc_free 0.943 _refine.B_iso_mean 21.934 _refine.aniso_B[1][1] 0.32 _refine.aniso_B[2][2] -0.50 _refine.aniso_B[3][3] 0.18 _refine.aniso_B[1][2] 0.00 _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' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 0.153 _refine.pdbx_overall_ESU_R_Free 0.136 _refine.overall_SU_ML 0.096 _refine.overall_SU_B 3.128 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 739 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 48 _refine_hist.number_atoms_solvent 120 _refine_hist.number_atoms_total 907 _refine_hist.d_res_high 1.86 _refine_hist.d_res_low 33.08 # 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 0.018 0.022 ? 815 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.776 2.117 ? 1125 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 21.004 5.000 ? 100 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.602 22.424 ? 33 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 13.139 15.000 ? 105 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 23.240 15.000 ? 7 'X-RAY DIFFRACTION' ? r_chiral_restr 0.133 0.200 ? 106 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 661 'X-RAY DIFFRACTION' ? r_nbd_refined 0.264 0.200 ? 406 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.304 0.200 ? 547 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.228 0.200 ? 92 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.228 0.200 ? 87 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.195 0.200 ? 37 'X-RAY DIFFRACTION' ? r_mcbond_it 0.983 1.500 ? 513 'X-RAY DIFFRACTION' ? r_mcangle_it 1.420 2.000 ? 795 'X-RAY DIFFRACTION' ? r_scbond_it 2.283 3.000 ? 349 'X-RAY DIFFRACTION' ? r_scangle_it 3.389 4.500 ? 328 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.857 _refine_ls_shell.d_res_low 1.906 _refine_ls_shell.number_reflns_R_work 536 _refine_ls_shell.R_factor_R_work 0.26 _refine_ls_shell.percent_reflns_obs 96.56 _refine_ls_shell.R_factor_R_free 0.445 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 25 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 327 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3DP5 _struct.title 'Crystal structure of Geobacter sulfurreducens OmcF with N-terminal Strep-tag II' _struct.pdbx_descriptor 'Cytochrome c family protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DP5 _struct_keywords.pdbx_keywords 'ELECTRON TRANSPORT' _struct_keywords.text 'c-type cytochrome, Fe SAD phasing, dissimilatory metal reduction, Geobacter sulfurreducens, ELECTRON TRANSPORT' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 12 ? ALA A 16 ? GLY A -9 ALA A -5 5 ? 5 HELX_P HELX_P2 2 GLY A 21 ? CYS A 30 ? GLY A 26 CYS A 35 1 ? 10 HELX_P HELX_P3 3 HIS A 34 ? GLY A 38 ? HIS A 39 GLY A 43 5 ? 5 HELX_P HELX_P4 4 ALA A 48 ? ASN A 55 ? ALA A 53 ASN A 60 1 ? 8 HELX_P HELX_P5 5 THR A 59 ? ILE A 67 ? THR A 64 ILE A 72 1 ? 9 HELX_P HELX_P6 6 PRO A 83 ? PHE A 98 ? PRO A 88 PHE A 103 1 ? 16 # _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 ? ? A HIS 34 NE2 ? ? ? 1_555 C HEC . FE ? ? A HIS 39 A HEC 122 1_555 ? ? ? ? ? ? ? 2.042 ? metalc2 metalc ? ? A MET 74 SD ? ? ? 1_555 C HEC . FE ? ? A MET 79 A HEC 122 1_555 ? ? ? ? ? ? ? 2.377 ? covale1 covale none ? A CYS 30 SG ? ? ? 1_555 C HEC . CAB ? ? A CYS 35 A HEC 122 1_555 ? ? ? ? ? ? ? 1.951 ? covale2 covale none ? A CYS 33 SG ? ? ? 1_555 C HEC . CAC ? ? A CYS 38 A HEC 122 1_555 ? ? ? ? ? ? ? 2.114 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? # 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 ? ? ? ? 11 'BINDING SITE FOR RESIDUE SO4 A 1' AC2 Software ? ? ? ? 21 'BINDING SITE FOR RESIDUE HEM A 122' # 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 11 ARG A 51 ? ARG A 56 . ? 4_457 ? 2 AC1 11 ALA A 54 ? ALA A 59 . ? 4_457 ? 3 AC1 11 GLY A 78 ? GLY A 83 . ? 1_555 ? 4 AC1 11 GLU A 79 ? GLU A 84 . ? 1_555 ? 5 AC1 11 ALA A 80 ? ALA A 85 . ? 1_555 ? 6 AC1 11 MET A 81 ? MET A 86 . ? 1_555 ? 7 AC1 11 HOH D . ? HOH A 133 . ? 1_555 ? 8 AC1 11 HOH D . ? HOH A 163 . ? 4_457 ? 9 AC1 11 HOH D . ? HOH A 169 . ? 1_555 ? 10 AC1 11 HOH D . ? HOH A 174 . ? 1_555 ? 11 AC1 11 HOH D . ? HOH A 237 . ? 1_555 ? 12 AC2 21 HIS A 6 ? HIS A -15 . ? 2_656 ? 13 AC2 21 HIS A 29 ? HIS A 34 . ? 1_555 ? 14 AC2 21 CYS A 30 ? CYS A 35 . ? 1_555 ? 15 AC2 21 CYS A 33 ? CYS A 38 . ? 1_555 ? 16 AC2 21 HIS A 34 ? HIS A 39 . ? 1_555 ? 17 AC2 21 ASN A 39 ? ASN A 44 . ? 1_555 ? 18 AC2 21 HIS A 42 ? HIS A 47 . ? 1_555 ? 19 AC2 21 LYS A 45 ? LYS A 50 . ? 1_555 ? 20 AC2 21 LEU A 47 ? LEU A 52 . ? 1_555 ? 21 AC2 21 ASN A 55 ? ASN A 60 . ? 1_555 ? 22 AC2 21 ILE A 57 ? ILE A 62 . ? 1_555 ? 23 AC2 21 TYR A 66 ? TYR A 71 . ? 1_555 ? 24 AC2 21 PRO A 72 ? PRO A 77 . ? 1_555 ? 25 AC2 21 GLY A 73 ? GLY A 78 . ? 1_555 ? 26 AC2 21 MET A 74 ? MET A 79 . ? 1_555 ? 27 AC2 21 ILE A 90 ? ILE A 95 . ? 1_555 ? 28 AC2 21 HOH D . ? HOH A 129 . ? 3_657 ? 29 AC2 21 HOH D . ? HOH A 136 . ? 1_555 ? 30 AC2 21 HOH D . ? HOH A 144 . ? 2_656 ? 31 AC2 21 HOH D . ? HOH A 195 . ? 3_657 ? 32 AC2 21 HOH D . ? HOH A 217 . ? 1_555 ? # _database_PDB_matrix.entry_id 3DP5 _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 3DP5 _atom_sites.fract_transf_matrix[1][1] 0.018700 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.024922 _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] 0.023761 _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 ALA 1 -20 -20 ALA ALA A . n A 1 2 ALA 2 -19 -19 ALA ALA A . n A 1 3 SER 3 -18 -18 SER SER A . n A 1 4 TRP 4 -17 -17 TRP TRP A . n A 1 5 SER 5 -16 -16 SER SER A . n A 1 6 HIS 6 -15 -15 HIS HIS A . n A 1 7 PRO 7 -14 -14 PRO PRO A . n A 1 8 GLN 8 -13 -13 GLN GLN A . n A 1 9 PHE 9 -12 -12 PHE PHE A . n A 1 10 GLU 10 -11 -11 GLU GLU A . n A 1 11 LYS 11 -10 -10 LYS LYS A . n A 1 12 GLY 12 -9 -9 GLY GLY A . n A 1 13 ALA 13 -8 -8 ALA ALA A . n A 1 14 GLU 14 -7 -7 GLU GLU A . n A 1 15 THR 15 -6 -6 THR THR A . n A 1 16 ALA 16 -5 -5 ALA ALA A . n A 1 17 VAL 17 -4 -4 VAL VAL A . n A 1 18 PRO 18 -3 -3 PRO PRO A . n A 1 19 ASN 19 -2 -2 ASN ASN A . n A 1 20 SER 20 -1 -1 SER SER A . n A 1 21 GLY 21 26 26 GLY GLY A . n A 1 22 GLY 22 27 27 GLY GLY A . n A 1 23 GLY 23 28 28 GLY GLY A . n A 1 24 GLU 24 29 29 GLU GLU A . n A 1 25 LEU 25 30 30 LEU LEU A . n A 1 26 PHE 26 31 31 PHE PHE A . n A 1 27 ALA 27 32 32 ALA ALA A . n A 1 28 THR 28 33 33 THR THR A . n A 1 29 HIS 29 34 34 HIS HIS A . n A 1 30 CYS 30 35 35 CYS CYS A . n A 1 31 ALA 31 36 36 ALA ALA A . n A 1 32 GLY 32 37 37 GLY GLY A . n A 1 33 CYS 33 38 38 CYS CYS A . n A 1 34 HIS 34 39 39 HIS HIS A . n A 1 35 PRO 35 40 40 PRO PRO A . n A 1 36 GLN 36 41 41 GLN GLN A . n A 1 37 GLY 37 42 42 GLY GLY A . n A 1 38 GLY 38 43 43 GLY GLY A . n A 1 39 ASN 39 44 44 ASN ASN A . n A 1 40 THR 40 45 45 THR THR A . n A 1 41 VAL 41 46 46 VAL VAL A . n A 1 42 HIS 42 47 47 HIS HIS A . n A 1 43 PRO 43 48 48 PRO PRO A . n A 1 44 GLU 44 49 49 GLU GLU A . n A 1 45 LYS 45 50 50 LYS LYS A . n A 1 46 THR 46 51 51 THR THR A . n A 1 47 LEU 47 52 52 LEU LEU A . n A 1 48 ALA 48 53 53 ALA ALA A . n A 1 49 ARG 49 54 54 ARG ARG A . n A 1 50 ALA 50 55 55 ALA ALA A . n A 1 51 ARG 51 56 56 ARG ARG A . n A 1 52 ARG 52 57 57 ARG ARG A . n A 1 53 GLU 53 58 58 GLU GLU A . n A 1 54 ALA 54 59 59 ALA ALA A . n A 1 55 ASN 55 60 60 ASN ASN A . n A 1 56 GLY 56 61 61 GLY GLY A . n A 1 57 ILE 57 62 62 ILE ILE A . n A 1 58 ARG 58 63 63 ARG ARG A . n A 1 59 THR 59 64 64 THR THR A . n A 1 60 VAL 60 65 65 VAL VAL A . n A 1 61 ARG 61 66 66 ARG ARG A . n A 1 62 ASP 62 67 67 ASP ASP A . n A 1 63 VAL 63 68 68 VAL VAL A . n A 1 64 ALA 64 69 69 ALA ALA A . n A 1 65 ALA 65 70 70 ALA ALA A . n A 1 66 TYR 66 71 71 TYR TYR A . n A 1 67 ILE 67 72 72 ILE ILE A . n A 1 68 ARG 68 73 73 ARG ARG A . n A 1 69 ASN 69 74 74 ASN ASN A . n A 1 70 PRO 70 75 75 PRO PRO A . n A 1 71 GLY 71 76 76 GLY GLY A . n A 1 72 PRO 72 77 77 PRO PRO A . n A 1 73 GLY 73 78 78 GLY GLY A . n A 1 74 MET 74 79 79 MET MET A . n A 1 75 PRO 75 80 80 PRO PRO A . n A 1 76 ALA 76 81 81 ALA ALA A . n A 1 77 PHE 77 82 82 PHE PHE A . n A 1 78 GLY 78 83 83 GLY GLY A . n A 1 79 GLU 79 84 84 GLU GLU A . n A 1 80 ALA 80 85 85 ALA ALA A . n A 1 81 MET 81 86 86 MET MET A . n A 1 82 ILE 82 87 87 ILE ILE A . n A 1 83 PRO 83 88 88 PRO PRO A . n A 1 84 PRO 84 89 89 PRO PRO A . n A 1 85 ALA 85 90 90 ALA ALA A . n A 1 86 ASP 86 91 91 ASP ASP A . n A 1 87 ALA 87 92 92 ALA ALA A . n A 1 88 LEU 88 93 93 LEU LEU A . n A 1 89 LYS 89 94 94 LYS LYS A . n A 1 90 ILE 90 95 95 ILE ILE A . n A 1 91 GLY 91 96 96 GLY GLY A . n A 1 92 GLU 92 97 97 GLU GLU A . n A 1 93 TYR 93 98 98 TYR TYR A . n A 1 94 VAL 94 99 99 VAL VAL A . n A 1 95 VAL 95 100 100 VAL VAL A . n A 1 96 ALA 96 101 101 ALA ALA A . n A 1 97 SER 97 102 102 SER SER A . n A 1 98 PHE 98 103 103 PHE PHE A . n A 1 99 PRO 99 104 104 PRO PRO 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 SO4 1 1 1 SO4 SO4 A . C 3 HEC 1 122 122 HEC HEM A . D 4 HOH 1 123 1 HOH HOH A . D 4 HOH 2 124 2 HOH HOH A . D 4 HOH 3 125 3 HOH HOH A . D 4 HOH 4 126 4 HOH HOH A . D 4 HOH 5 127 5 HOH HOH A . D 4 HOH 6 128 6 HOH HOH A . D 4 HOH 7 129 7 HOH HOH A . D 4 HOH 8 130 8 HOH HOH A . D 4 HOH 9 131 9 HOH HOH A . D 4 HOH 10 132 10 HOH HOH A . D 4 HOH 11 133 11 HOH HOH A . D 4 HOH 12 134 12 HOH HOH A . D 4 HOH 13 135 13 HOH HOH A . D 4 HOH 14 136 14 HOH HOH A . D 4 HOH 15 137 15 HOH HOH A . D 4 HOH 16 138 16 HOH HOH A . D 4 HOH 17 139 17 HOH HOH A . D 4 HOH 18 140 18 HOH HOH A . D 4 HOH 19 141 19 HOH HOH A . D 4 HOH 20 142 20 HOH HOH A . D 4 HOH 21 143 21 HOH HOH A . D 4 HOH 22 144 22 HOH HOH A . D 4 HOH 23 145 23 HOH HOH A . D 4 HOH 24 146 24 HOH HOH A . D 4 HOH 25 147 25 HOH HOH A . D 4 HOH 26 148 26 HOH HOH A . D 4 HOH 27 149 27 HOH HOH A . D 4 HOH 28 150 28 HOH HOH A . D 4 HOH 29 151 29 HOH HOH A . D 4 HOH 30 152 30 HOH HOH A . D 4 HOH 31 153 31 HOH HOH A . D 4 HOH 32 154 32 HOH HOH A . D 4 HOH 33 155 33 HOH HOH A . D 4 HOH 34 156 34 HOH HOH A . D 4 HOH 35 157 35 HOH HOH A . D 4 HOH 36 158 36 HOH HOH A . D 4 HOH 37 159 37 HOH HOH A . D 4 HOH 38 160 38 HOH HOH A . D 4 HOH 39 161 39 HOH HOH A . D 4 HOH 40 162 40 HOH HOH A . D 4 HOH 41 163 41 HOH HOH A . D 4 HOH 42 164 42 HOH HOH A . D 4 HOH 43 165 43 HOH HOH A . D 4 HOH 44 166 44 HOH HOH A . D 4 HOH 45 167 45 HOH HOH A . D 4 HOH 46 168 46 HOH HOH A . D 4 HOH 47 169 47 HOH HOH A . D 4 HOH 48 170 48 HOH HOH A . D 4 HOH 49 171 49 HOH HOH A . D 4 HOH 50 172 50 HOH HOH A . D 4 HOH 51 173 51 HOH HOH A . D 4 HOH 52 174 52 HOH HOH A . D 4 HOH 53 175 53 HOH HOH A . D 4 HOH 54 176 54 HOH HOH A . D 4 HOH 55 177 55 HOH HOH A . D 4 HOH 56 178 56 HOH HOH A . D 4 HOH 57 179 57 HOH HOH A . D 4 HOH 58 180 58 HOH HOH A . D 4 HOH 59 181 59 HOH HOH A . D 4 HOH 60 182 60 HOH HOH A . D 4 HOH 61 183 61 HOH HOH A . D 4 HOH 62 184 62 HOH HOH A . D 4 HOH 63 185 63 HOH HOH A . D 4 HOH 64 186 64 HOH HOH A . D 4 HOH 65 187 65 HOH HOH A . D 4 HOH 66 188 66 HOH HOH A . D 4 HOH 67 189 67 HOH HOH A . D 4 HOH 68 190 68 HOH HOH A . D 4 HOH 69 191 69 HOH HOH A . D 4 HOH 70 192 70 HOH HOH A . D 4 HOH 71 193 71 HOH HOH A . D 4 HOH 72 194 72 HOH HOH A . D 4 HOH 73 195 73 HOH HOH A . D 4 HOH 74 196 74 HOH HOH A . D 4 HOH 75 197 75 HOH HOH A . D 4 HOH 76 198 76 HOH HOH A . D 4 HOH 77 199 77 HOH HOH A . D 4 HOH 78 200 78 HOH HOH A . D 4 HOH 79 202 80 HOH HOH A . D 4 HOH 80 203 81 HOH HOH A . D 4 HOH 81 204 82 HOH HOH A . D 4 HOH 82 205 83 HOH HOH A . D 4 HOH 83 206 84 HOH HOH A . D 4 HOH 84 207 85 HOH HOH A . D 4 HOH 85 208 86 HOH HOH A . D 4 HOH 86 209 87 HOH HOH A . D 4 HOH 87 210 88 HOH HOH A . D 4 HOH 88 211 89 HOH HOH A . D 4 HOH 89 212 90 HOH HOH A . D 4 HOH 90 213 91 HOH HOH A . D 4 HOH 91 215 93 HOH HOH A . D 4 HOH 92 216 94 HOH HOH A . D 4 HOH 93 217 95 HOH HOH A . D 4 HOH 94 218 96 HOH HOH A . D 4 HOH 95 219 97 HOH HOH A . D 4 HOH 96 221 99 HOH HOH A . D 4 HOH 97 222 100 HOH HOH A . D 4 HOH 98 223 101 HOH HOH A . D 4 HOH 99 224 102 HOH HOH A . D 4 HOH 100 225 103 HOH HOH A . D 4 HOH 101 226 104 HOH HOH A . D 4 HOH 102 227 105 HOH HOH A . D 4 HOH 103 228 106 HOH HOH A . D 4 HOH 104 229 107 HOH HOH A . D 4 HOH 105 230 108 HOH HOH A . D 4 HOH 106 231 109 HOH HOH A . D 4 HOH 107 232 110 HOH HOH A . D 4 HOH 108 233 111 HOH HOH A . D 4 HOH 109 234 112 HOH HOH A . D 4 HOH 110 235 113 HOH HOH A . D 4 HOH 111 236 114 HOH HOH A . D 4 HOH 112 237 115 HOH HOH A . D 4 HOH 113 238 116 HOH HOH A . D 4 HOH 114 239 117 HOH HOH A . D 4 HOH 115 240 118 HOH HOH A . D 4 HOH 116 241 119 HOH HOH A . D 4 HOH 117 242 120 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 34 ? A HIS 39 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NA ? C HEC . ? A HEC 122 ? 1_555 89.5 ? 2 NE2 ? A HIS 34 ? A HIS 39 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NB ? C HEC . ? A HEC 122 ? 1_555 88.7 ? 3 NA ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NB ? C HEC . ? A HEC 122 ? 1_555 89.9 ? 4 NE2 ? A HIS 34 ? A HIS 39 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NC ? C HEC . ? A HEC 122 ? 1_555 89.3 ? 5 NA ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NC ? C HEC . ? A HEC 122 ? 1_555 178.6 ? 6 NB ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 NC ? C HEC . ? A HEC 122 ? 1_555 89.4 ? 7 NE2 ? A HIS 34 ? A HIS 39 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 ND ? C HEC . ? A HEC 122 ? 1_555 87.6 ? 8 NA ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 ND ? C HEC . ? A HEC 122 ? 1_555 90.3 ? 9 NB ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 ND ? C HEC . ? A HEC 122 ? 1_555 176.4 ? 10 NC ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 ND ? C HEC . ? A HEC 122 ? 1_555 90.3 ? 11 NE2 ? A HIS 34 ? A HIS 39 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 SD ? A MET 74 ? A MET 79 ? 1_555 176.2 ? 12 NA ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 SD ? A MET 74 ? A MET 79 ? 1_555 87.3 ? 13 NB ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 SD ? A MET 74 ? A MET 79 ? 1_555 93.4 ? 14 NC ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 SD ? A MET 74 ? A MET 79 ? 1_555 93.9 ? 15 ND ? C HEC . ? A HEC 122 ? 1_555 FE ? C HEC . ? A HEC 122 ? 1_555 SD ? A MET 74 ? A MET 79 ? 1_555 90.3 ? # 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 2008-09-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 2 0 2019-10-02 # _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' 'Version format compliance' 2 3 'Structure model' 'Atomic model' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Non-polymer description' 6 3 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' atom_site 2 3 'Structure model' chem_comp 3 3 'Structure model' entity 4 3 'Structure model' pdbx_entity_nonpoly 5 3 'Structure model' pdbx_nonpoly_scheme 6 3 'Structure model' pdbx_struct_conn_angle 7 3 '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 3 'Structure model' '_atom_site.B_iso_or_equiv' 2 3 'Structure model' '_atom_site.Cartn_x' 3 3 'Structure model' '_atom_site.Cartn_y' 4 3 'Structure model' '_atom_site.Cartn_z' 5 3 'Structure model' '_atom_site.auth_atom_id' 6 3 'Structure model' '_atom_site.auth_comp_id' 7 3 'Structure model' '_atom_site.label_atom_id' 8 3 'Structure model' '_atom_site.label_comp_id' 9 3 'Structure model' '_atom_site.type_symbol' 10 3 'Structure model' '_chem_comp.formula' 11 3 'Structure model' '_chem_comp.formula_weight' 12 3 'Structure model' '_chem_comp.id' 13 3 'Structure model' '_chem_comp.name' 14 3 'Structure model' '_chem_comp.pdbx_synonyms' 15 3 'Structure model' '_entity.formula_weight' 16 3 'Structure model' '_entity.pdbx_description' 17 3 'Structure model' '_pdbx_entity_nonpoly.comp_id' 18 3 'Structure model' '_pdbx_entity_nonpoly.name' 19 3 'Structure model' '_pdbx_nonpoly_scheme.mon_id' 20 3 'Structure model' '_pdbx_nonpoly_scheme.pdb_mon_id' 21 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 22 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 23 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 24 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 25 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 26 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 27 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 28 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 MAR345dtb 'data collection' . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 SHARP phasing . ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 NH1 A ARG 66 ? B O A HOH 238 ? ? 1.69 2 1 NE A ARG 66 ? B O A HOH 168 ? ? 2.10 3 1 OE1 A GLN 41 ? ? O A HOH 229 ? ? 2.15 # 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 ASN A 44 ? ? -162.15 109.64 2 1 LYS A 50 ? ? -109.31 61.81 3 1 ASN A 74 ? ? -157.30 65.68 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 GLY _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 83 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 GLU _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 84 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -130.95 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 'HEME C' HEC 4 water HOH #