data_1PYZ # _entry.id 1PYZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.295 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1PYZ RCSB RCSB019710 WWPDB D_1000019710 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1PYZ _pdbx_database_status.recvd_initial_deposition_date 2003-07-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Di Costanzo, L.' 1 'Geremia, S.' 2 'Randaccio, L.' 3 'Nastri, F.' 4 'Maglio, O.' 5 'Lombardi, A.' 6 'Pavone, V.' 7 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Miniaturized heme proteins: crystal structure of Co(III)-mimochrome IV.' J.Biol.Inorg.Chem. 9 1017 1027 2004 JJBCFA GW 0949-8257 2154 ? 15551102 10.1007/s00775-004-0600-x 1 ;"Design of a new mimochrome with unique topology" ; 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Di Costanzo, L.' 1 primary 'Geremia, S.' 2 primary 'Randaccio, L.' 3 primary 'Nastri, F.' 4 primary 'Maglio, O.' 5 primary 'Lombardi, A.' 6 primary 'Pavone, V.' 7 1 'Lombardi, A.' 8 1 'Nastri, F.' 9 1 'Marasco, D.' 10 1 'Maglio, O.' 11 1 'De Sanctis, G.' 12 1 'Sinibaldi, F.' 13 1 'Santucci, R.' 14 1 'Coletta, M.' 15 1 'Pavone, V.' 16 # _cell.entry_id 1PYZ _cell.length_a 65.536 _cell.length_b 65.536 _cell.length_c 23.529 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _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 1PYZ _symmetry.space_group_name_H-M 'P 64 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _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 syn 'MIMOCHROME IV, MINIATURIZED METALLOPROTEIN' 1125.240 2 ? ? ? ? 2 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 3 non-polymer syn 'CO(III)-(DEUTEROPORPHYRIN IX)' 567.501 1 ? ? ? ? 4 water nat water 18.015 67 ? ? ? ? # _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 '(ACE)ESQLHSNKR(NH2)' _entity_poly.pdbx_seq_one_letter_code_can XESQLHSNKRX _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ACE n 1 2 GLU n 1 3 SER n 1 4 GLN n 1 5 LEU n 1 6 HIS n 1 7 SER n 1 8 ASN n 1 9 LYS n 1 10 ARG n 1 11 NH2 n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1PYZ _struct_ref.pdbx_db_accession 1PYZ _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1PYZ A 1 ? 11 ? 1PYZ 0 ? 10 ? 0 10 2 1 1PYZ B 1 ? 11 ? 1PYZ 0 ? 10 ? 0 10 # 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 ACE non-polymer . 'ACETYL GROUP' ? 'C2 H4 O' 44.053 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 DEU non-polymer . 'CO(III)-(DEUTEROPORPHYRIN IX)' ? 'C30 H28 Co N4 O4 5' 567.501 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 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 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # _exptl.entry_id 1PYZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.70 _exptl_crystal.density_percent_sol 55.0 _exptl_crystal.description 'FOUR DATA SET WHERE COLLECTED WITH VAWELENGHT 1.000(A) 1.606(A),1.612(A)' _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'water and 2-propanol, EVAPORATION' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2001-04-21 _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 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.000 1.0 2 1.604 1.0 3 1.606 1.0 4 1.612 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ELETTRA BEAMLINE 5.2R' _diffrn_source.pdbx_synchrotron_site ELETTRA _diffrn_source.pdbx_synchrotron_beamline 5.2R _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.000, 1.604, 1.606, 1.612' # _reflns.entry_id 1PYZ _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 16.4 _reflns.d_resolution_high 1.250 _reflns.number_obs 8061 _reflns.number_all ? _reflns.percent_possible_obs 94.4 _reflns.pdbx_Rmerge_I_obs 0.093 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.0 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 15.0 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.25 _reflns_shell.d_res_low 1.32 _reflns_shell.percent_possible_all 86.4 _reflns_shell.Rmerge_I_obs 0.636 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.1 _reflns_shell.pdbx_redundancy 9.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1PYZ _refine.ls_number_reflns_obs 7651 _refine.ls_number_reflns_all 7651 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 4 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 16.4 _refine.ls_d_res_high 1.25 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.173 _refine.ls_R_factor_R_free 0.179 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 314 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details 'ANISOTROPIC REFINEMENT FOR COBALT AND CHLORIDE IONS. NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO COBALT ATOM.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MAD on the cobalt edge' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_ESU_R ? _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 160 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 38 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 265 _refine_hist.d_res_high 1.25 _refine_hist.d_res_low 16.4 # 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 s_bond_d 0.010 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 2.60 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1PYZ _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.185 _pdbx_refine.free_R_factor_no_cutoff 0.188 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 396 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.17 _pdbx_refine.free_R_factor_4sig_cutoff 0.179 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.000 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 314 _pdbx_refine.number_reflns_obs_4sig_cutoff 6269 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 1PYZ _struct.title 'CRYSTALLOGRAPHIC STRUCTURE OF MIMOCHROME IV' _struct.pdbx_descriptor 'MIMOCHROME IV, MINIATURIZED METALLOPROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PYZ _struct_keywords.pdbx_keywords 'METAL BINDING PROTEIN' _struct_keywords.text 'MINIATURIZED METALLOPROTEIN, MAD ON THE COBALT EDGE, METAL BINDING PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 3 ? ARG A 10 ? SER A 2 ARG A 9 1 ? 8 HELX_P HELX_P2 2 SER B 3 ? ARG B 10 ? SER B 2 ARG B 9 1 ? 8 # _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 ? ? A ACE 1 C ? ? ? 1_555 A GLU 2 N ? ? A ACE 0 A GLU 1 1_555 ? ? ? ? ? ? ? 1.323 ? covale2 covale ? ? A ARG 10 C ? ? ? 1_555 A NH2 11 N ? ? A ARG 9 A NH2 10 1_555 ? ? ? ? ? ? ? 1.316 ? covale3 covale ? ? B ACE 1 C ? ? ? 1_555 B GLU 2 N ? ? B ACE 0 B GLU 1 1_555 ? ? ? ? ? ? ? 1.309 ? covale4 covale ? ? B ARG 10 C ? ? ? 1_555 B NH2 11 N ? ? B ARG 9 B NH2 10 1_555 ? ? ? ? ? ? ? 1.332 ? metalc1 metalc ? ? A HIS 6 NE2 ? ? ? 1_555 D DEU . CO ? ? A HIS 5 A DEU 101 1_555 ? ? ? ? ? ? ? 1.982 ? metalc2 metalc ? ? B HIS 6 NE2 ? ? ? 1_555 D DEU . CO ? ? B HIS 5 A DEU 101 1_555 ? ? ? ? ? ? ? 1.925 ? # 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 ? ? ? ? 4 'BINDING SITE FOR RESIDUE CL A 68' AC2 Software ? ? ? ? 10 'BINDING SITE FOR RESIDUE DEU 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 4 LYS A 9 ? LYS A 8 . ? 12_544 ? 2 AC1 4 LYS A 9 ? LYS A 8 . ? 1_555 ? 3 AC1 4 LYS B 9 ? LYS B 8 . ? 12_544 ? 4 AC1 4 LYS B 9 ? LYS B 8 . ? 1_555 ? 5 AC2 10 ACE A 1 ? ACE A 0 . ? 11_555 ? 6 AC2 10 HIS A 6 ? HIS A 5 . ? 1_555 ? 7 AC2 10 LYS A 9 ? LYS A 8 . ? 1_555 ? 8 AC2 10 ARG A 10 ? ARG A 9 . ? 1_555 ? 9 AC2 10 HOH E . ? HOH A 103 . ? 1_555 ? 10 AC2 10 HOH E . ? HOH A 104 . ? 1_555 ? 11 AC2 10 GLU B 2 ? GLU B 1 . ? 8_435 ? 12 AC2 10 HIS B 6 ? HIS B 5 . ? 1_555 ? 13 AC2 10 LYS B 9 ? LYS B 8 . ? 1_555 ? 14 AC2 10 ARG B 10 ? ARG B 9 . ? 8_435 ? # _database_PDB_matrix.entry_id 1PYZ _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 1PYZ _atom_sites.fract_transf_matrix[1][1] 0.015259 _atom_sites.fract_transf_matrix[1][2] 0.008810 _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] 0.017619 _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] 0.042501 _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 CL CO H N O # 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 ACE 1 0 0 ACE ACE A . n A 1 2 GLU 2 1 1 GLU GLU A . n A 1 3 SER 3 2 2 SER SER A . n A 1 4 GLN 4 3 3 GLN GLN A . n A 1 5 LEU 5 4 4 LEU LEU A . n A 1 6 HIS 6 5 5 HIS HIS A . n A 1 7 SER 7 6 6 SER SER A . n A 1 8 ASN 8 7 7 ASN ASN A . n A 1 9 LYS 9 8 8 LYS LYS A . n A 1 10 ARG 10 9 9 ARG ARG A . n A 1 11 NH2 11 10 10 NH2 NH2 A . n B 1 1 ACE 1 0 0 ACE ACE B . n B 1 2 GLU 2 1 1 GLU GLU B . n B 1 3 SER 3 2 2 SER SER B . n B 1 4 GLN 4 3 3 GLN GLN B . n B 1 5 LEU 5 4 4 LEU LEU B . n B 1 6 HIS 6 5 5 HIS HIS B . n B 1 7 SER 7 6 6 SER SER B . n B 1 8 ASN 8 7 7 ASN ASN B . n B 1 9 LYS 9 8 8 LYS LYS B . n B 1 10 ARG 10 9 9 ARG ARG B . n B 1 11 NH2 11 10 10 NH2 NH2 B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 CL 1 68 68 CL CL A . D 3 DEU 1 101 19 DEU DEU A . E 4 HOH 1 102 1 HOH HOH A . E 4 HOH 2 103 2 HOH HOH A . E 4 HOH 3 104 3 HOH HOH A . E 4 HOH 4 105 4 HOH HOH A . E 4 HOH 5 106 5 HOH HOH A . E 4 HOH 6 107 6 HOH HOH A . E 4 HOH 7 108 10 HOH HOH A . E 4 HOH 8 109 12 HOH HOH A . E 4 HOH 9 110 14 HOH HOH A . E 4 HOH 10 111 16 HOH HOH A . E 4 HOH 11 112 19 HOH HOH A . E 4 HOH 12 113 20 HOH HOH A . E 4 HOH 13 114 21 HOH HOH A . E 4 HOH 14 115 22 HOH HOH A . E 4 HOH 15 116 23 HOH HOH A . E 4 HOH 16 117 24 HOH HOH A . E 4 HOH 17 118 25 HOH HOH A . E 4 HOH 18 119 27 HOH HOH A . E 4 HOH 19 120 28 HOH HOH A . E 4 HOH 20 121 29 HOH HOH A . E 4 HOH 21 122 30 HOH HOH A . E 4 HOH 22 123 37 HOH HOH A . E 4 HOH 23 124 40 HOH HOH A . E 4 HOH 24 125 43 HOH HOH A . E 4 HOH 25 126 46 HOH HOH A . E 4 HOH 26 127 47 HOH HOH A . E 4 HOH 27 128 48 HOH HOH A . E 4 HOH 28 129 51 HOH HOH A . E 4 HOH 29 130 52 HOH HOH A . E 4 HOH 30 131 55 HOH HOH A . E 4 HOH 31 132 56 HOH HOH A . E 4 HOH 32 133 61 HOH HOH A . E 4 HOH 33 134 62 HOH HOH A . E 4 HOH 34 135 65 HOH HOH A . E 4 HOH 35 136 66 HOH HOH A . F 4 HOH 1 11 7 HOH HOH B . F 4 HOH 2 12 8 HOH HOH B . F 4 HOH 3 13 9 HOH HOH B . F 4 HOH 4 14 11 HOH HOH B . F 4 HOH 5 15 13 HOH HOH B . F 4 HOH 6 16 15 HOH HOH B . F 4 HOH 7 17 17 HOH HOH B . F 4 HOH 8 18 18 HOH HOH B . F 4 HOH 9 19 26 HOH HOH B . F 4 HOH 10 20 31 HOH HOH B . F 4 HOH 11 21 32 HOH HOH B . F 4 HOH 12 22 33 HOH HOH B . F 4 HOH 13 23 34 HOH HOH B . F 4 HOH 14 24 35 HOH HOH B . F 4 HOH 15 25 36 HOH HOH B . F 4 HOH 16 26 38 HOH HOH B . F 4 HOH 17 27 39 HOH HOH B . F 4 HOH 18 28 41 HOH HOH B . F 4 HOH 19 29 42 HOH HOH B . F 4 HOH 20 30 44 HOH HOH B . F 4 HOH 21 31 45 HOH HOH B . F 4 HOH 22 32 49 HOH HOH B . F 4 HOH 23 33 50 HOH HOH B . F 4 HOH 24 34 53 HOH HOH B . F 4 HOH 25 35 54 HOH HOH B . F 4 HOH 26 36 57 HOH HOH B . F 4 HOH 27 37 58 HOH HOH B . F 4 HOH 28 38 59 HOH HOH B . F 4 HOH 29 39 60 HOH HOH B . F 4 HOH 30 40 63 HOH HOH B . F 4 HOH 31 41 64 HOH HOH B . F 4 HOH 32 42 67 HOH HOH B . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 software_defined_assembly PISA tetrameric 4 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F 2 1,2 A,B,C,D,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 3460 ? 2 MORE -46 ? 2 'SSA (A^2)' 3500 ? # 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' 12_544 x,x-y-1,-z-1/3 0.5000000000 0.8660254038 0.0000000000 32.7680000000 0.8660254038 -0.5000000000 0.0000000000 -56.7558408624 0.0000000000 0.0000000000 -1.0000000000 -7.8430000000 # 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 CL 68 ? C CL . 2 1 B HOH 18 ? F HOH . 3 1 B HOH 31 ? F 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 NE2 ? A HIS 6 ? A HIS 5 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NA ? D DEU . ? A DEU 101 ? 1_555 91.3 ? 2 NE2 ? A HIS 6 ? A HIS 5 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NB ? D DEU . ? A DEU 101 ? 1_555 89.1 ? 3 NA ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NB ? D DEU . ? A DEU 101 ? 1_555 89.2 ? 4 NE2 ? A HIS 6 ? A HIS 5 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NC ? D DEU . ? A DEU 101 ? 1_555 89.4 ? 5 NA ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NC ? D DEU . ? A DEU 101 ? 1_555 179.3 ? 6 NB ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NC ? D DEU . ? A DEU 101 ? 1_555 90.6 ? 7 NE2 ? A HIS 6 ? A HIS 5 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 ND ? D DEU . ? A DEU 101 ? 1_555 89.7 ? 8 NA ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 ND ? D DEU . ? A DEU 101 ? 1_555 89.8 ? 9 NB ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 ND ? D DEU . ? A DEU 101 ? 1_555 178.5 ? 10 NC ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 ND ? D DEU . ? A DEU 101 ? 1_555 90.4 ? 11 NE2 ? A HIS 6 ? A HIS 5 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NE2 ? B HIS 6 ? B HIS 5 ? 1_555 177.1 ? 12 NA ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NE2 ? B HIS 6 ? B HIS 5 ? 1_555 89.9 ? 13 NB ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NE2 ? B HIS 6 ? B HIS 5 ? 1_555 93.6 ? 14 NC ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NE2 ? B HIS 6 ? B HIS 5 ? 1_555 89.4 ? 15 ND ? D DEU . ? A DEU 101 ? 1_555 CO ? D DEU . ? A DEU 101 ? 1_555 NE2 ? B HIS 6 ? B HIS 5 ? 1_555 87.6 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2004-12-14 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2018-06-27 # _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' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' Advisory 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' pdbx_unobs_or_zero_occ_atoms 3 5 'Structure model' struct_conn # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 4 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_software.name' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 MLPHARE phasing . ? 3 RSPS 'model building' 'FROM CCP4.SHELXL FOR THE REFINEMEN' ? 4 SHELX refinement 'VERSION 97-1' ? 5 SHELXL-97 refinement . ? 6 # 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 NZ A LYS 8 ? ? CGD A DEU 101 ? ? 1.34 2 1 NZ B LYS 8 ? ? CGA A DEU 101 ? ? 1.38 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 A DEU 101 ? O1D ? D DEU 1 O1D 2 1 N 1 A DEU 101 ? O2A ? D DEU 1 O2A # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 'CO(III)-(DEUTEROPORPHYRIN IX)' DEU 4 water HOH #