data_3VYM # _entry.id 3VYM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3VYM RCSB RCSB095663 WWPDB D_1000095663 # _pdbx_database_status.entry_id 3VYM _pdbx_database_status.status_code REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2012-09-28 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hayashi, Y.' 1 'Nagao, S.' 2 'Osuka, H.' 3 'Komori, H.' 4 'Higuchi, Y.' 5 'Hirota, S.' 6 # _citation.id primary _citation.title 'Domain Swapping of the Heme and N-Terminal alpha-Helix in Hydrogenobacter thermophilus Cytochrome c(552) Dimer' _citation.journal_abbrev Biochemistry _citation.journal_volume 51 _citation.page_first 8608 _citation.page_last 8616 _citation.year 2012 _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 23035813 _citation.pdbx_database_id_DOI 10.1021/bi3011303 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hayashi, Y.' 1 primary 'Nagao, S.' 2 primary 'Osuka, H.' 3 primary 'Komori, H.' 4 primary 'Higuchi, Y.' 5 primary 'Hirota, S.' 6 # _cell.length_a 46.148 _cell.length_b 46.148 _cell.length_c 78.407 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3VYM _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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.space_group_name_H-M 'P 31 2 1' _symmetry.entry_id 3VYM _symmetry.Int_Tables_number 152 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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-552' 8586.015 1 ? ? ? ? 2 non-polymer syn 'HEME C' 618.503 1 ? ? ? ? 3 water nat water 18.015 32 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Cytochrome c552' # _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 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK _entity_poly.pdbx_seq_one_letter_code_can NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK _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 ASN n 1 2 GLU n 1 3 GLN n 1 4 LEU n 1 5 ALA n 1 6 LYS n 1 7 GLN n 1 8 LYS n 1 9 GLY n 1 10 CYS n 1 11 MET n 1 12 ALA n 1 13 CYS n 1 14 HIS n 1 15 ASP n 1 16 LEU n 1 17 LYS n 1 18 ALA n 1 19 LYS n 1 20 LYS n 1 21 VAL n 1 22 GLY n 1 23 PRO n 1 24 ALA n 1 25 TYR n 1 26 ALA n 1 27 ASP n 1 28 VAL n 1 29 ALA n 1 30 LYS n 1 31 LYS n 1 32 TYR n 1 33 ALA n 1 34 GLY n 1 35 ARG n 1 36 LYS n 1 37 ASP n 1 38 ALA n 1 39 VAL n 1 40 ASP n 1 41 TYR n 1 42 LEU n 1 43 ALA n 1 44 GLY n 1 45 LYS n 1 46 ILE n 1 47 LYS n 1 48 LYS n 1 49 GLY n 1 50 GLY n 1 51 SER n 1 52 GLY n 1 53 VAL n 1 54 TRP n 1 55 GLY n 1 56 SER n 1 57 VAL n 1 58 PRO n 1 59 MET n 1 60 PRO n 1 61 PRO n 1 62 GLN n 1 63 ASN n 1 64 VAL n 1 65 THR n 1 66 ASP n 1 67 ALA n 1 68 GLU n 1 69 ALA n 1 70 LYS n 1 71 GLN n 1 72 LEU n 1 73 ALA n 1 74 GLN n 1 75 TRP n 1 76 ILE n 1 77 LEU n 1 78 SER n 1 79 ILE n 1 80 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 'HTH_0988, Hydth_0984' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain TK-6 _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 'Hydrogenobacter thermophilus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 608538 _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 JCB387 _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 pKO2 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code CY552_HYDTT _struct_ref.pdbx_db_accession P15452 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK ; _struct_ref.pdbx_align_begin 19 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3VYM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 80 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P15452 _struct_ref_seq.db_align_beg 19 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 98 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 80 # 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 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.crystals_number 1 _exptl.entry_id 3VYM _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity 1.641 _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 2.81 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 56.18 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _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.pH 7.0 _exptl_crystal_grow.temp 295 _exptl_crystal_grow.pdbx_details ;100mM HEPES buffer, 800mM ammonium sulfate, 45% (v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K ; _exptl_crystal_grow.temp_details ? _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 CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-06-19 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si double crystal' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 'SPRING-8 BEAMLINE BL38B1' _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL38B1 # _reflns.entry_id 3VYM _reflns.d_resolution_high 2.000 _reflns.d_resolution_low 50.000 _reflns.number_obs 6916 _reflns.pdbx_Rmerge_I_obs 0.083 _reflns.pdbx_netI_over_sigmaI 9.600 _reflns.pdbx_chi_squared 1.531 _reflns.pdbx_redundancy 10.100 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I -3 _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.000 2.070 ? ? ? ? 0.859 ? ? 1.043 10.000 ? ? ? 670 ? ? ? ? 100.000 ? ? 1 1 2.070 2.150 ? ? ? ? 0.688 ? ? 1.159 10.300 ? ? ? 658 ? ? ? ? 100.000 ? ? 2 1 2.150 2.250 ? ? ? ? 0.511 ? ? 1.083 10.400 ? ? ? 677 ? ? ? ? 100.000 ? ? 3 1 2.250 2.370 ? ? ? ? 0.388 ? ? 1.169 10.400 ? ? ? 678 ? ? ? ? 100.000 ? ? 4 1 2.370 2.520 ? ? ? ? 0.251 ? ? 1.222 10.300 ? ? ? 686 ? ? ? ? 99.900 ? ? 5 1 2.520 2.710 ? ? ? ? 0.190 ? ? 1.464 10.400 ? ? ? 699 ? ? ? ? 100.000 ? ? 6 1 2.710 2.990 ? ? ? ? 0.134 ? ? 1.926 10.300 ? ? ? 664 ? ? ? ? 100.000 ? ? 7 1 2.990 3.420 ? ? ? ? 0.080 ? ? 2.119 10.100 ? ? ? 708 ? ? ? ? 99.900 ? ? 8 1 3.420 4.310 ? ? ? ? 0.055 ? ? 2.181 9.900 ? ? ? 711 ? ? ? ? 100.000 ? ? 9 1 4.310 50.000 ? ? ? ? 0.040 ? ? 1.910 9.500 ? ? ? 765 ? ? ? ? 99.100 ? ? 10 1 # _refine.entry_id 3VYM _refine.ls_d_res_high 2.0000 _refine.ls_d_res_low 39.9700 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.2200 _refine.ls_number_reflns_obs 6526 _refine.ls_number_reflns_all 6853 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2067 _refine.ls_R_factor_R_work 0.2040 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2635 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.8000 _refine.ls_number_reflns_R_free 327 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 38.3436 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.4300 _refine.aniso_B[2][2] 1.4300 _refine.aniso_B[3][3] -2.1500 _refine.aniso_B[1][2] 0.7200 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9580 _refine.correlation_coeff_Fo_to_Fc_free 0.9170 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.1760 _refine.pdbx_overall_ESU_R_Free 0.1730 _refine.overall_SU_ML 0.1290 _refine.overall_SU_B 4.7220 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 74.820 _refine.B_iso_min 19.660 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 601 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 43 _refine_hist.number_atoms_solvent 32 _refine_hist.number_atoms_total 676 _refine_hist.d_res_high 2.0000 _refine_hist.d_res_low 39.9700 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 668 0.022 0.022 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 914 2.165 2.174 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 81 7.050 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 22 38.931 26.364 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 117 18.659 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 1 8.256 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 88 0.137 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 499 0.010 0.021 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 399 1.303 1.500 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 631 2.280 2.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 269 3.235 3.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 282 5.005 4.500 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.0000 _refine_ls_shell.d_res_low 2.0520 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 98.1500 _refine_ls_shell.number_reflns_R_work 462 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2670 _refine_ls_shell.R_factor_R_free 0.2940 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 16 _refine_ls_shell.R_factor_R_free_error 0.173 _refine_ls_shell.number_reflns_all 478 _refine_ls_shell.number_reflns_obs 478 _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3VYM _struct.title 'Dimeric Hydrogenobacter thermophilus cytochrome c552' _struct.pdbx_descriptor 'Cytochrome c-552' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VYM _struct_keywords.text 'Electron Transport' _struct_keywords.pdbx_keywords '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 ? # _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 ASN A 1 ? LYS A 8 ? ASN A 1 LYS A 8 1 ? 8 HELX_P HELX_P2 2 GLY A 9 ? CYS A 13 ? GLY A 9 CYS A 13 5 ? 5 HELX_P HELX_P3 3 ALA A 24 ? ALA A 33 ? ALA A 24 ALA A 33 1 ? 10 HELX_P HELX_P4 4 ASP A 37 ? GLY A 49 ? ASP A 37 GLY A 49 1 ? 13 HELX_P HELX_P5 5 THR A 65 ? SER A 78 ? THR A 65 SER A 78 1 ? 14 # _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 14 NE2 ? ? ? 1_555 B HEC . FE ? ? A HIS 14 A HEC 101 1_555 ? ? ? ? ? ? ? 1.886 ? covale1 covale ? ? A CYS 10 SG ? ? ? 1_555 B HEC . CAB ? ? A CYS 10 A HEC 101 1_555 ? ? ? ? ? ? ? 1.734 ? covale2 covale ? ? A CYS 13 SG ? ? ? 1_555 B HEC . CAC ? ? A CYS 13 A HEC 101 1_555 ? ? ? ? ? ? ? 2.119 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 19 _struct_site.details 'BINDING SITE FOR RESIDUE HEC A 101' # 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 19 CYS A 10 ? CYS A 10 . ? 1_555 ? 2 AC1 19 CYS A 13 ? CYS A 13 . ? 1_555 ? 3 AC1 19 HIS A 14 ? HIS A 14 . ? 1_555 ? 4 AC1 19 PRO A 23 ? PRO A 23 . ? 4_645 ? 5 AC1 19 TYR A 25 ? TYR A 25 . ? 4_645 ? 6 AC1 19 TYR A 32 ? TYR A 32 . ? 4_645 ? 7 AC1 19 TYR A 41 ? TYR A 41 . ? 4_645 ? 8 AC1 19 LYS A 45 ? LYS A 45 . ? 4_645 ? 9 AC1 19 ILE A 46 ? ILE A 46 . ? 4_645 ? 10 AC1 19 SER A 51 ? SER A 51 . ? 4_645 ? 11 AC1 19 GLY A 52 ? GLY A 52 . ? 4_645 ? 12 AC1 19 VAL A 53 ? VAL A 53 . ? 4_645 ? 13 AC1 19 TRP A 54 ? TRP A 54 . ? 4_645 ? 14 AC1 19 GLY A 55 ? GLY A 55 . ? 4_645 ? 15 AC1 19 VAL A 57 ? VAL A 57 . ? 4_645 ? 16 AC1 19 MET A 59 ? MET A 59 . ? 4_645 ? 17 AC1 19 GLN A 62 ? GLN A 62 . ? 4_645 ? 18 AC1 19 HOH C . ? HOH A 201 . ? 1_555 ? 19 AC1 19 HOH C . ? HOH A 203 . ? 4_645 ? # _atom_sites.entry_id 3VYM _atom_sites.fract_transf_matrix[1][1] 0.021669 _atom_sites.fract_transf_matrix[1][2] 0.012511 _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] 0.025022 _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] 0.012754 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # 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 ASN 1 1 1 ASN ASN A . n A 1 2 GLU 2 2 2 GLU GLU A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 GLN 7 7 7 GLN GLN A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 CYS 10 10 10 CYS CYS A . n A 1 11 MET 11 11 11 MET MET A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 CYS 13 13 13 CYS CYS A . n A 1 14 HIS 14 14 14 HIS HIS A . n A 1 15 ASP 15 15 15 ASP ASP A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 LYS 19 19 19 LYS LYS A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 PRO 23 23 23 PRO PRO A . n A 1 24 ALA 24 24 24 ALA ALA A . n A 1 25 TYR 25 25 25 TYR TYR A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 ASP 27 27 27 ASP ASP A . n A 1 28 VAL 28 28 28 VAL VAL A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 LYS 30 30 30 LYS LYS A . n A 1 31 LYS 31 31 31 LYS LYS A . n A 1 32 TYR 32 32 32 TYR TYR A . n A 1 33 ALA 33 33 33 ALA ALA A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 LYS 36 36 36 LYS LYS 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 VAL 39 39 39 VAL VAL A . n A 1 40 ASP 40 40 40 ASP ASP A . n A 1 41 TYR 41 41 41 TYR TYR A . n A 1 42 LEU 42 42 42 LEU LEU A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 LYS 45 45 45 LYS LYS A . n A 1 46 ILE 46 46 46 ILE ILE A . n A 1 47 LYS 47 47 47 LYS LYS A . n A 1 48 LYS 48 48 48 LYS LYS A . n A 1 49 GLY 49 49 49 GLY GLY A . n A 1 50 GLY 50 50 50 GLY GLY A . n A 1 51 SER 51 51 51 SER SER A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 VAL 53 53 53 VAL VAL A . n A 1 54 TRP 54 54 54 TRP TRP A . n A 1 55 GLY 55 55 55 GLY GLY A . n A 1 56 SER 56 56 56 SER SER A . n A 1 57 VAL 57 57 57 VAL VAL A . n A 1 58 PRO 58 58 58 PRO PRO A . n A 1 59 MET 59 59 59 MET MET A . n A 1 60 PRO 60 60 60 PRO PRO A . n A 1 61 PRO 61 61 61 PRO PRO A . n A 1 62 GLN 62 62 62 GLN GLN A . n A 1 63 ASN 63 63 63 ASN ASN A . n A 1 64 VAL 64 64 64 VAL VAL A . n A 1 65 THR 65 65 65 THR THR A . n A 1 66 ASP 66 66 66 ASP ASP A . n A 1 67 ALA 67 67 67 ALA ALA A . n A 1 68 GLU 68 68 68 GLU GLU A . n A 1 69 ALA 69 69 69 ALA ALA A . n A 1 70 LYS 70 70 70 LYS LYS A . n A 1 71 GLN 71 71 71 GLN GLN A . n A 1 72 LEU 72 72 72 LEU LEU A . n A 1 73 ALA 73 73 73 ALA ALA A . n A 1 74 GLN 74 74 74 GLN GLN A . n A 1 75 TRP 75 75 75 TRP TRP A . n A 1 76 ILE 76 76 76 ILE ILE A . n A 1 77 LEU 77 77 77 LEU LEU A . n A 1 78 SER 78 78 78 SER SER A . n A 1 79 ILE 79 79 79 ILE ILE A . n A 1 80 LYS 80 80 80 LYS LYS 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 1 101 81 HEC HEC A . C 3 HOH 1 201 1 HOH HOH A . C 3 HOH 2 202 2 HOH HOH A . C 3 HOH 3 203 3 HOH HOH A . C 3 HOH 4 204 4 HOH HOH A . C 3 HOH 5 205 5 HOH HOH A . C 3 HOH 6 206 6 HOH HOH A . C 3 HOH 7 207 7 HOH HOH A . C 3 HOH 8 208 8 HOH HOH A . C 3 HOH 9 209 9 HOH HOH A . C 3 HOH 10 210 10 HOH HOH A . C 3 HOH 11 211 11 HOH HOH A . C 3 HOH 12 212 12 HOH HOH A . C 3 HOH 13 213 20 HOH HOH A . C 3 HOH 14 214 21 HOH HOH A . C 3 HOH 15 215 22 HOH HOH A . C 3 HOH 16 216 23 HOH HOH A . C 3 HOH 17 217 26 HOH HOH A . C 3 HOH 18 218 28 HOH HOH A . C 3 HOH 19 219 30 HOH HOH A . C 3 HOH 20 220 31 HOH HOH A . C 3 HOH 21 221 32 HOH HOH A . C 3 HOH 22 222 33 HOH HOH A . C 3 HOH 23 223 34 HOH HOH A . C 3 HOH 24 224 35 HOH HOH A . C 3 HOH 25 225 36 HOH HOH A . C 3 HOH 26 226 37 HOH HOH A . C 3 HOH 27 227 38 HOH HOH A . C 3 HOH 28 228 39 HOH HOH A . C 3 HOH 29 229 40 HOH HOH A . C 3 HOH 30 230 42 HOH HOH A . C 3 HOH 31 231 43 HOH HOH A . C 3 HOH 32 232 44 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 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 # 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)' 5310 ? 1 MORE -63 ? 1 'SSA (A^2)' 9440 ? # 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' 4_645 y+1,x-1,-z -0.5000000000 0.8660254038 0.0000000000 69.2220000000 0.8660254038 0.5000000000 0.0000000000 -39.9653403338 0.0000000000 0.0000000000 -1.0000000000 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 14 ? A HIS 14 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NA ? B HEC . ? A HEC 101 ? 1_555 89.6 ? 2 NE2 ? A HIS 14 ? A HIS 14 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NB ? B HEC . ? A HEC 101 ? 1_555 86.5 ? 3 NA ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NB ? B HEC . ? A HEC 101 ? 1_555 90.5 ? 4 NE2 ? A HIS 14 ? A HIS 14 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NC ? B HEC . ? A HEC 101 ? 1_555 88.0 ? 5 NA ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NC ? B HEC . ? A HEC 101 ? 1_555 177.0 ? 6 NB ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 NC ? B HEC . ? A HEC 101 ? 1_555 91.1 ? 7 NE2 ? A HIS 14 ? A HIS 14 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 ND ? B HEC . ? A HEC 101 ? 1_555 92.3 ? 8 NA ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 ND ? B HEC . ? A HEC 101 ? 1_555 87.7 ? 9 NB ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 ND ? B HEC . ? A HEC 101 ? 1_555 177.7 ? 10 NC ? B HEC . ? A HEC 101 ? 1_555 FE ? B HEC . ? A HEC 101 ? 1_555 ND ? B HEC . ? A HEC 101 ? 1_555 90.7 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-11-07 2 'Structure model' 1 1 2017-11-22 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 4 REFMAC 5.5.0109 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'HEME C' HEC 3 water HOH #