data_3DLD # _entry.id 3DLD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3DLD RCSB RCSB048182 WWPDB D_1000048182 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2016-10-12 _pdbx_database_PDB_obs_spr.pdb_id 5E5D _pdbx_database_PDB_obs_spr.replace_pdb_id 3DLD _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 3DLD _pdbx_database_status.recvd_initial_deposition_date 2008-06-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 'Ngo, H.P.-T.' 1 'Kim, J.K.' 2 'Jung, J.H.' 3 'Kang, L.W.' 4 # _citation.id primary _citation.title 'Crystal structure of peptide deformylase, Xoo1075, from Xanthomonas oryzae pv. oryzae KACC10331' _citation.journal_abbrev 'to be published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ngo, H.P.-T.' 1 primary 'Kim, J.K.' 2 primary 'Jung, J.H.' 3 primary 'Kang, L.W.' 4 # _cell.entry_id 3DLD _cell.length_a 58.968 _cell.length_b 58.968 _cell.length_c 266.285 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3DLD _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _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 'Peptide deformylase' 19097.656 1 3.5.1.88 ? 'residues in database 42-212' ? 2 non-polymer syn 'CADMIUM ION' 112.411 3 ? ? ? ? 3 water nat water 18.015 115 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Polypeptide deformylase' # _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 ;MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTAL ANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDT FGFDDVLSYDL ; _entity_poly.pdbx_seq_one_letter_code_can ;MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTAL ANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDT FGFDDVLSYDL ; _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 MET n 1 2 ILE n 1 3 ARG n 1 4 ASP n 1 5 ILE n 1 6 ILE n 1 7 ARG n 1 8 MET n 1 9 GLY n 1 10 ASP n 1 11 LYS n 1 12 ARG n 1 13 LEU n 1 14 LEU n 1 15 ARG n 1 16 VAL n 1 17 ALA n 1 18 PRO n 1 19 GLN n 1 20 VAL n 1 21 THR n 1 22 ASN n 1 23 LEU n 1 24 GLY n 1 25 SER n 1 26 ALA n 1 27 GLU n 1 28 LEU n 1 29 HIS n 1 30 ALA n 1 31 LEU n 1 32 VAL n 1 33 SER n 1 34 ASP n 1 35 MET n 1 36 PHE n 1 37 GLU n 1 38 THR n 1 39 MET n 1 40 GLY n 1 41 ALA n 1 42 ALA n 1 43 HIS n 1 44 GLY n 1 45 VAL n 1 46 GLY n 1 47 LEU n 1 48 ALA n 1 49 ALA n 1 50 PRO n 1 51 GLN n 1 52 ILE n 1 53 ALA n 1 54 VAL n 1 55 ASP n 1 56 LEU n 1 57 GLN n 1 58 LEU n 1 59 MET n 1 60 VAL n 1 61 PHE n 1 62 GLY n 1 63 PHE n 1 64 GLU n 1 65 ALA n 1 66 SER n 1 67 GLU n 1 68 ARG n 1 69 TYR n 1 70 PRO n 1 71 GLU n 1 72 ALA n 1 73 PRO n 1 74 ALA n 1 75 VAL n 1 76 PRO n 1 77 LEU n 1 78 THR n 1 79 ALA n 1 80 LEU n 1 81 ALA n 1 82 ASN n 1 83 ALA n 1 84 GLN n 1 85 ILE n 1 86 GLU n 1 87 PRO n 1 88 LEU n 1 89 SER n 1 90 ASP n 1 91 GLU n 1 92 MET n 1 93 GLU n 1 94 ASN n 1 95 GLY n 1 96 TRP n 1 97 GLU n 1 98 GLY n 1 99 CYS n 1 100 LEU n 1 101 SER n 1 102 ILE n 1 103 PRO n 1 104 GLY n 1 105 LEU n 1 106 ARG n 1 107 ALA n 1 108 VAL n 1 109 ILE n 1 110 PRO n 1 111 ARG n 1 112 TYR n 1 113 ARG n 1 114 TYR n 1 115 ILE n 1 116 ARG n 1 117 TYR n 1 118 ARG n 1 119 GLY n 1 120 PHE n 1 121 ALA n 1 122 PRO n 1 123 ASP n 1 124 GLY n 1 125 SER n 1 126 PRO n 1 127 ILE n 1 128 GLU n 1 129 ARG n 1 130 GLU n 1 131 ALA n 1 132 GLU n 1 133 GLY n 1 134 PHE n 1 135 HIS n 1 136 ALA n 1 137 ARG n 1 138 VAL n 1 139 VAL n 1 140 GLN n 1 141 HIS n 1 142 GLU n 1 143 TYR n 1 144 ASP n 1 145 HIS n 1 146 LEU n 1 147 VAL n 1 148 GLY n 1 149 ARG n 1 150 LEU n 1 151 TYR n 1 152 PRO n 1 153 SER n 1 154 ARG n 1 155 ILE n 1 156 GLU n 1 157 ASN n 1 158 PHE n 1 159 ASP n 1 160 THR n 1 161 PHE n 1 162 GLY n 1 163 PHE n 1 164 ASP n 1 165 ASP n 1 166 VAL n 1 167 LEU n 1 168 SER n 1 169 TYR n 1 170 ASP n 1 171 LEU 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 'def, XOO1075' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain KACC10331 _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 'Xanthomonas oryzae pv. oryzae' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 64187 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q5H3Z2_XANOR _struct_ref.pdbx_db_accession Q5H3Z2 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTAL ANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDT FGFDDVLSYDL ; _struct_ref.pdbx_align_begin 42 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DLD _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 171 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5H3Z2 _struct_ref_seq.db_align_beg 42 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 212 _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 171 # 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 CD non-polymer . 'CADMIUM ION' ? 'Cd 2' 112.411 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3DLD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.50 _exptl_crystal.density_percent_sol 64.85 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 287 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details '0.05M Cadmium sulfate, 0.1M HEPES, 2.0M Sodium acetate trihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-6A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-6A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00000 # _reflns.entry_id 3DLD _reflns.observed_criterion_sigma_F 1 _reflns.observed_criterion_sigma_I 1 _reflns.d_resolution_high 2.6 _reflns.d_resolution_low 50 _reflns.number_all 9007 _reflns.number_obs 9007 _reflns.percent_possible_obs 96.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 2.6 _reflns_shell.d_res_low ? _reflns_shell.percent_possible_all 96.87 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _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 3DLD _refine.ls_number_reflns_obs 8577 _refine.ls_number_reflns_all 9004 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 36.86 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 96.87 _refine.ls_R_factor_obs 0.19459 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19237 _refine.ls_R_factor_R_free 0.23968 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 427 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.938 _refine.correlation_coeff_Fo_to_Fc_free 0.914 _refine.B_iso_mean 29.880 _refine.aniso_B[1][1] 0.05 _refine.aniso_B[2][2] 0.05 _refine.aniso_B[3][3] -0.07 _refine.aniso_B[1][2] 0.02 _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 'MOLECULAR REPLACEMENT' _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 0.373 _refine.pdbx_overall_ESU_R_Free 0.264 _refine.overall_SU_ML 0.169 _refine.overall_SU_B 7.842 _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 1335 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 115 _refine_hist.number_atoms_total 1453 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 36.86 # 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 0.020 0.022 ? 1368 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.931 1.967 ? 1857 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.232 5.000 ? 169 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 35.466 22.899 ? 69 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.435 15.000 ? 215 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 21.348 15.000 ? 14 'X-RAY DIFFRACTION' ? r_chiral_restr 0.154 0.200 ? 198 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 1082 'X-RAY DIFFRACTION' ? r_nbd_refined 0.230 0.200 ? 657 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.315 0.200 ? 944 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.193 0.200 ? 105 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.055 0.200 ? 1 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.167 0.200 ? 40 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.185 0.200 ? 10 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined 0.076 0.200 ? 2 'X-RAY DIFFRACTION' ? r_mcbond_it 1.299 1.500 ? 872 'X-RAY DIFFRACTION' ? r_mcangle_it 1.803 2.000 ? 1358 'X-RAY DIFFRACTION' ? r_scbond_it 2.926 3.000 ? 557 'X-RAY DIFFRACTION' ? r_scangle_it 4.445 4.500 ? 499 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.601 _refine_ls_shell.d_res_low 2.668 _refine_ls_shell.number_reflns_R_work 609 _refine_ls_shell.R_factor_R_work 0.229 _refine_ls_shell.percent_reflns_obs 97.26 _refine_ls_shell.R_factor_R_free 0.242 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 29 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3DLD _struct.title 'Crystal structure of peptide deformylase, Xoo1075, from Xanthomonas oryzae pv. oryzae KACC10331' _struct.pdbx_descriptor 'Peptide deformylase (E.C.3.5.1.88)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DLD _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'Bacterial blight, peptide deformylase, Xoo1075, Xanthomonas oryzae pv. oryzae KACC10331, Hydrolase' # 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 2 ? D N N 2 ? E 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 ASP A 10 ? ARG A 15 ? ASP A 10 ARG A 15 5 ? 6 HELX_P HELX_P2 2 SER A 25 ? ALA A 42 ? SER A 25 ALA A 42 1 ? 18 HELX_P HELX_P3 3 PRO A 50 ? ALA A 53 ? PRO A 50 ALA A 53 5 ? 4 HELX_P HELX_P4 4 GLY A 133 ? VAL A 147 ? GLY A 133 VAL A 147 1 ? 15 HELX_P HELX_P5 5 LEU A 150 ? ILE A 155 ? LEU A 150 ILE A 155 5 ? 6 HELX_P HELX_P6 6 ASN A 157 ? PHE A 161 ? ASN A 157 PHE A 161 5 ? 5 # _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 GLU 128 OE1 ? ? ? 1_555 B CD . CD ? ? A GLU 128 A CD 172 1_555 ? ? ? ? ? ? ? 2.480 ? metalc2 metalc ? ? A GLU 130 OE2 ? ? ? 1_555 B CD . CD ? ? A GLU 130 A CD 172 1_555 ? ? ? ? ? ? ? 2.493 ? metalc3 metalc ? ? A GLU 132 OE1 ? ? ? 1_555 D CD . CD ? ? A GLU 132 A CD 174 1_555 ? ? ? ? ? ? ? 2.201 ? metalc4 metalc ? ? A HIS 141 NE2 ? ? ? 1_555 C CD . CD ? ? A HIS 141 A CD 173 1_555 ? ? ? ? ? ? ? 2.310 ? metalc5 metalc ? ? A HIS 145 NE2 ? ? ? 1_555 C CD . CD ? ? A HIS 145 A CD 173 1_555 ? ? ? ? ? ? ? 2.345 ? metalc6 metalc ? ? B CD . CD ? ? ? 1_555 E HOH . O ? ? A CD 172 A HOH 182 1_555 ? ? ? ? ? ? ? 2.398 ? metalc7 metalc ? ? C CD . CD ? ? ? 1_555 E HOH . O ? ? A CD 173 A HOH 177 1_555 ? ? ? ? ? ? ? 2.144 ? metalc8 metalc ? ? A CYS 99 SG ? ? ? 1_555 C CD . CD ? ? A CYS 99 A CD 173 1_555 ? ? ? ? ? ? ? 2.395 ? metalc9 metalc ? ? A GLU 130 OE1 ? ? ? 1_555 B CD . CD ? ? A GLU 130 A CD 172 1_555 ? ? ? ? ? ? ? 2.636 ? metalc10 metalc ? ? D CD . CD ? ? ? 1_555 E HOH . O ? ? A CD 174 A HOH 232 1_555 ? ? ? ? ? ? ? 2.663 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLY A 46 ? ALA A 48 ? GLY A 46 ALA A 48 A 2 LEU A 58 ? PHE A 63 ? LEU A 58 PHE A 63 A 3 VAL A 75 ? PRO A 87 ? VAL A 75 PRO A 87 A 4 TYR A 114 ? PHE A 120 ? TYR A 114 PHE A 120 A 5 PRO A 126 ? GLU A 132 ? PRO A 126 GLU A 132 B 1 MET A 92 ? CYS A 99 ? MET A 92 CYS A 99 B 2 ILE A 102 ? TYR A 112 ? ILE A 102 TYR A 112 B 3 GLY A 162 ? PHE A 163 ? GLY A 162 PHE A 163 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU A 47 ? N LEU A 47 O VAL A 60 ? O VAL A 60 A 2 3 N PHE A 61 ? N PHE A 61 O THR A 78 ? O THR A 78 A 3 4 N ALA A 81 ? N ALA A 81 O PHE A 120 ? O PHE A 120 A 4 5 N ILE A 115 ? N ILE A 115 O ALA A 131 ? O ALA A 131 B 1 2 N GLU A 97 ? N GLU A 97 O ALA A 107 ? O ALA A 107 B 2 3 N ARG A 106 ? N ARG A 106 O GLY A 162 ? O GLY A 162 # 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 ? ? ? ? 5 'BINDING SITE FOR RESIDUE CD A 172' AC2 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE CD A 173' AC3 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE CD A 174' # 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 5 HIS A 43 ? HIS A 43 . ? 8_545 ? 2 AC1 5 GLU A 128 ? GLU A 128 . ? 1_555 ? 3 AC1 5 GLU A 130 ? GLU A 130 . ? 1_555 ? 4 AC1 5 HOH E . ? HOH A 182 . ? 1_555 ? 5 AC1 5 HOH E . ? HOH A 209 . ? 8_545 ? 6 AC2 5 GLN A 51 ? GLN A 51 . ? 1_555 ? 7 AC2 5 CYS A 99 ? CYS A 99 . ? 1_555 ? 8 AC2 5 HIS A 141 ? HIS A 141 . ? 1_555 ? 9 AC2 5 HIS A 145 ? HIS A 145 . ? 1_555 ? 10 AC2 5 HOH E . ? HOH A 177 . ? 1_555 ? 11 AC3 4 MET A 1 ? MET A 1 . ? 8_545 ? 12 AC3 4 GLU A 37 ? GLU A 37 . ? 8_545 ? 13 AC3 4 GLU A 132 ? GLU A 132 . ? 1_555 ? 14 AC3 4 HOH E . ? HOH A 232 . ? 1_555 ? # _database_PDB_matrix.entry_id 3DLD _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 3DLD _atom_sites.fract_transf_matrix[1][1] 0.016958 _atom_sites.fract_transf_matrix[1][2] 0.009791 _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] 0.019582 _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] 0.003755 _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 CD 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 MET 1 1 1 MET MET A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 ARG 3 3 3 ARG ARG A . n A 1 4 ASP 4 4 4 ASP ASP A . n A 1 5 ILE 5 5 5 ILE ILE A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 ARG 7 7 7 ARG ARG A . n A 1 8 MET 8 8 8 MET MET A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 ASP 10 10 10 ASP ASP A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 ARG 12 12 12 ARG ARG A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 ARG 15 15 15 ARG ARG A . n A 1 16 VAL 16 16 16 VAL VAL A . n A 1 17 ALA 17 17 17 ALA ALA A . n A 1 18 PRO 18 18 18 PRO PRO A . n A 1 19 GLN 19 19 19 GLN GLN A . n A 1 20 VAL 20 20 20 VAL VAL A . n A 1 21 THR 21 21 21 THR THR A . n A 1 22 ASN 22 22 22 ASN ASN A . n A 1 23 LEU 23 23 23 LEU LEU A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 SER 25 25 25 SER SER A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 LEU 28 28 28 LEU LEU A . n A 1 29 HIS 29 29 29 HIS HIS A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 LEU 31 31 31 LEU LEU A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 SER 33 33 33 SER SER A . n A 1 34 ASP 34 34 34 ASP ASP A . n A 1 35 MET 35 35 35 MET MET A . n A 1 36 PHE 36 36 36 PHE PHE A . n A 1 37 GLU 37 37 37 GLU GLU A . n A 1 38 THR 38 38 38 THR THR A . n A 1 39 MET 39 39 39 MET MET A . n A 1 40 GLY 40 40 40 GLY GLY A . n A 1 41 ALA 41 41 41 ALA ALA A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 HIS 43 43 43 HIS HIS A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 VAL 45 45 45 VAL VAL A . n A 1 46 GLY 46 46 46 GLY GLY A . n A 1 47 LEU 47 47 47 LEU LEU A . n A 1 48 ALA 48 48 48 ALA ALA A . n A 1 49 ALA 49 49 49 ALA ALA A . n A 1 50 PRO 50 50 50 PRO PRO A . n A 1 51 GLN 51 51 51 GLN GLN A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 VAL 54 54 54 VAL VAL A . n A 1 55 ASP 55 55 55 ASP ASP A . n A 1 56 LEU 56 56 56 LEU LEU A . n A 1 57 GLN 57 57 57 GLN GLN A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 MET 59 59 59 MET MET A . n A 1 60 VAL 60 60 60 VAL VAL A . n A 1 61 PHE 61 61 61 PHE PHE A . n A 1 62 GLY 62 62 62 GLY GLY A . n A 1 63 PHE 63 63 63 PHE PHE A . n A 1 64 GLU 64 64 64 GLU GLU A . n A 1 65 ALA 65 65 65 ALA ALA A . n A 1 66 SER 66 66 66 SER SER A . n A 1 67 GLU 67 67 67 GLU GLU A . n A 1 68 ARG 68 68 68 ARG ARG A . n A 1 69 TYR 69 69 69 TYR TYR A . n A 1 70 PRO 70 70 70 PRO PRO A . n A 1 71 GLU 71 71 71 GLU GLU A . n A 1 72 ALA 72 72 72 ALA ALA A . n A 1 73 PRO 73 73 73 PRO PRO A . n A 1 74 ALA 74 74 74 ALA ALA A . n A 1 75 VAL 75 75 75 VAL VAL A . n A 1 76 PRO 76 76 76 PRO PRO A . n A 1 77 LEU 77 77 77 LEU LEU A . n A 1 78 THR 78 78 78 THR THR A . n A 1 79 ALA 79 79 79 ALA ALA A . n A 1 80 LEU 80 80 80 LEU LEU A . n A 1 81 ALA 81 81 81 ALA ALA A . n A 1 82 ASN 82 82 82 ASN ASN A . n A 1 83 ALA 83 83 83 ALA ALA A . n A 1 84 GLN 84 84 84 GLN GLN A . n A 1 85 ILE 85 85 85 ILE ILE A . n A 1 86 GLU 86 86 86 GLU GLU A . n A 1 87 PRO 87 87 87 PRO PRO A . n A 1 88 LEU 88 88 88 LEU LEU A . n A 1 89 SER 89 89 89 SER SER A . n A 1 90 ASP 90 90 90 ASP ASP A . n A 1 91 GLU 91 91 91 GLU GLU A . n A 1 92 MET 92 92 92 MET MET A . n A 1 93 GLU 93 93 93 GLU GLU A . n A 1 94 ASN 94 94 94 ASN ASN A . n A 1 95 GLY 95 95 95 GLY GLY A . n A 1 96 TRP 96 96 96 TRP TRP A . n A 1 97 GLU 97 97 97 GLU GLU A . n A 1 98 GLY 98 98 98 GLY GLY A . n A 1 99 CYS 99 99 99 CYS CYS A . n A 1 100 LEU 100 100 100 LEU LEU A . n A 1 101 SER 101 101 101 SER SER A . n A 1 102 ILE 102 102 102 ILE ILE A . n A 1 103 PRO 103 103 103 PRO PRO A . n A 1 104 GLY 104 104 104 GLY GLY A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 ARG 106 106 106 ARG ARG A . n A 1 107 ALA 107 107 107 ALA ALA A . n A 1 108 VAL 108 108 108 VAL VAL A . n A 1 109 ILE 109 109 109 ILE ILE A . n A 1 110 PRO 110 110 110 PRO PRO A . n A 1 111 ARG 111 111 111 ARG ARG A . n A 1 112 TYR 112 112 112 TYR TYR A . n A 1 113 ARG 113 113 113 ARG ARG A . n A 1 114 TYR 114 114 114 TYR TYR A . n A 1 115 ILE 115 115 115 ILE ILE A . n A 1 116 ARG 116 116 116 ARG ARG A . n A 1 117 TYR 117 117 117 TYR TYR A . n A 1 118 ARG 118 118 118 ARG ARG A . n A 1 119 GLY 119 119 119 GLY GLY A . n A 1 120 PHE 120 120 120 PHE PHE A . n A 1 121 ALA 121 121 121 ALA ALA A . n A 1 122 PRO 122 122 122 PRO PRO A . n A 1 123 ASP 123 123 123 ASP ASP A . n A 1 124 GLY 124 124 124 GLY GLY A . n A 1 125 SER 125 125 125 SER SER A . n A 1 126 PRO 126 126 126 PRO PRO A . n A 1 127 ILE 127 127 127 ILE ILE A . n A 1 128 GLU 128 128 128 GLU GLU A . n A 1 129 ARG 129 129 129 ARG ARG A . n A 1 130 GLU 130 130 130 GLU GLU A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 GLU 132 132 132 GLU GLU A . n A 1 133 GLY 133 133 133 GLY GLY A . n A 1 134 PHE 134 134 134 PHE PHE A . n A 1 135 HIS 135 135 135 HIS HIS A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 ARG 137 137 137 ARG ARG A . n A 1 138 VAL 138 138 138 VAL VAL A . n A 1 139 VAL 139 139 139 VAL VAL A . n A 1 140 GLN 140 140 140 GLN GLN A . n A 1 141 HIS 141 141 141 HIS HIS A . n A 1 142 GLU 142 142 142 GLU GLU A . n A 1 143 TYR 143 143 143 TYR TYR A . n A 1 144 ASP 144 144 144 ASP ASP A . n A 1 145 HIS 145 145 145 HIS HIS A . n A 1 146 LEU 146 146 146 LEU LEU A . n A 1 147 VAL 147 147 147 VAL VAL A . n A 1 148 GLY 148 148 148 GLY GLY A . n A 1 149 ARG 149 149 149 ARG ARG A . n A 1 150 LEU 150 150 150 LEU LEU A . n A 1 151 TYR 151 151 151 TYR TYR A . n A 1 152 PRO 152 152 152 PRO PRO A . n A 1 153 SER 153 153 153 SER SER A . n A 1 154 ARG 154 154 154 ARG ARG A . n A 1 155 ILE 155 155 155 ILE ILE A . n A 1 156 GLU 156 156 156 GLU GLU A . n A 1 157 ASN 157 157 157 ASN ASN A . n A 1 158 PHE 158 158 158 PHE PHE A . n A 1 159 ASP 159 159 159 ASP ASP A . n A 1 160 THR 160 160 160 THR THR A . n A 1 161 PHE 161 161 161 PHE PHE A . n A 1 162 GLY 162 162 162 GLY GLY A . n A 1 163 PHE 163 163 163 PHE PHE A . n A 1 164 ASP 164 164 164 ASP ASP A . n A 1 165 ASP 165 165 165 ASP ASP A . n A 1 166 VAL 166 166 166 VAL VAL A . n A 1 167 LEU 167 167 167 LEU LEU A . n A 1 168 SER 168 168 168 SER SER A . n A 1 169 TYR 169 169 169 TYR TYR A . n A 1 170 ASP 170 170 170 ASP ASP A . n A 1 171 LEU 171 171 ? ? ? 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 CD 1 172 1 CD CD A . C 2 CD 1 173 2 CD CD A . D 2 CD 1 174 3 CD CD A . E 3 HOH 1 175 1 HOH HOH A . E 3 HOH 2 176 2 HOH HOH A . E 3 HOH 3 177 3 HOH HOH A . E 3 HOH 4 178 4 HOH HOH A . E 3 HOH 5 179 5 HOH HOH A . E 3 HOH 6 180 6 HOH HOH A . E 3 HOH 7 181 7 HOH HOH A . E 3 HOH 8 182 8 HOH HOH A . E 3 HOH 9 183 9 HOH HOH A . E 3 HOH 10 184 10 HOH HOH A . E 3 HOH 11 185 11 HOH HOH A . E 3 HOH 12 186 12 HOH HOH A . E 3 HOH 13 187 13 HOH HOH A . E 3 HOH 14 188 14 HOH HOH A . E 3 HOH 15 189 15 HOH HOH A . E 3 HOH 16 190 16 HOH HOH A . E 3 HOH 17 191 17 HOH HOH A . E 3 HOH 18 192 18 HOH HOH A . E 3 HOH 19 193 19 HOH HOH A . E 3 HOH 20 194 20 HOH HOH A . E 3 HOH 21 195 21 HOH HOH A . E 3 HOH 22 196 22 HOH HOH A . E 3 HOH 23 197 23 HOH HOH A . E 3 HOH 24 198 24 HOH HOH A . E 3 HOH 25 199 25 HOH HOH A . E 3 HOH 26 200 26 HOH HOH A . E 3 HOH 27 201 27 HOH HOH A . E 3 HOH 28 202 28 HOH HOH A . E 3 HOH 29 203 29 HOH HOH A . E 3 HOH 30 204 30 HOH HOH A . E 3 HOH 31 205 31 HOH HOH A . E 3 HOH 32 206 32 HOH HOH A . E 3 HOH 33 207 33 HOH HOH A . E 3 HOH 34 208 34 HOH HOH A . E 3 HOH 35 209 35 HOH HOH A . E 3 HOH 36 210 36 HOH HOH A . E 3 HOH 37 211 37 HOH HOH A . E 3 HOH 38 212 38 HOH HOH A . E 3 HOH 39 213 39 HOH HOH A . E 3 HOH 40 214 40 HOH HOH A . E 3 HOH 41 215 41 HOH HOH A . E 3 HOH 42 216 42 HOH HOH A . E 3 HOH 43 217 43 HOH HOH A . E 3 HOH 44 218 44 HOH HOH A . E 3 HOH 45 219 45 HOH HOH A . E 3 HOH 46 220 46 HOH HOH A . E 3 HOH 47 221 47 HOH HOH A . E 3 HOH 48 222 48 HOH HOH A . E 3 HOH 49 223 49 HOH HOH A . E 3 HOH 50 224 50 HOH HOH A . E 3 HOH 51 225 51 HOH HOH A . E 3 HOH 52 226 52 HOH HOH A . E 3 HOH 53 227 53 HOH HOH A . E 3 HOH 54 228 54 HOH HOH A . E 3 HOH 55 229 55 HOH HOH A . E 3 HOH 56 230 56 HOH HOH A . E 3 HOH 57 231 57 HOH HOH A . E 3 HOH 58 232 58 HOH HOH A . E 3 HOH 59 233 59 HOH HOH A . E 3 HOH 60 234 60 HOH HOH A . E 3 HOH 61 235 61 HOH HOH A . E 3 HOH 62 236 62 HOH HOH A . E 3 HOH 63 237 63 HOH HOH A . E 3 HOH 64 238 64 HOH HOH A . E 3 HOH 65 239 65 HOH HOH A . E 3 HOH 66 240 66 HOH HOH A . E 3 HOH 67 241 67 HOH HOH A . E 3 HOH 68 242 68 HOH HOH A . E 3 HOH 69 243 69 HOH HOH A . E 3 HOH 70 244 70 HOH HOH A . E 3 HOH 71 245 71 HOH HOH A . E 3 HOH 72 246 72 HOH HOH A . E 3 HOH 73 247 73 HOH HOH A . E 3 HOH 74 248 74 HOH HOH A . E 3 HOH 75 249 75 HOH HOH A . E 3 HOH 76 250 76 HOH HOH A . E 3 HOH 77 251 77 HOH HOH A . E 3 HOH 78 252 78 HOH HOH A . E 3 HOH 79 253 79 HOH HOH A . E 3 HOH 80 254 80 HOH HOH A . E 3 HOH 81 255 81 HOH HOH A . E 3 HOH 82 256 82 HOH HOH A . E 3 HOH 83 257 83 HOH HOH A . E 3 HOH 84 258 84 HOH HOH A . E 3 HOH 85 259 85 HOH HOH A . E 3 HOH 86 260 86 HOH HOH A . E 3 HOH 87 261 87 HOH HOH A . E 3 HOH 88 262 88 HOH HOH A . E 3 HOH 89 263 89 HOH HOH A . E 3 HOH 90 264 90 HOH HOH A . E 3 HOH 91 265 91 HOH HOH A . E 3 HOH 92 266 92 HOH HOH A . E 3 HOH 93 267 93 HOH HOH A . E 3 HOH 94 268 94 HOH HOH A . E 3 HOH 95 269 95 HOH HOH A . E 3 HOH 96 270 96 HOH HOH A . E 3 HOH 97 271 97 HOH HOH A . E 3 HOH 98 272 98 HOH HOH A . E 3 HOH 99 273 99 HOH HOH A . E 3 HOH 100 274 100 HOH HOH A . E 3 HOH 101 275 101 HOH HOH A . E 3 HOH 102 276 102 HOH HOH A . E 3 HOH 103 277 103 HOH HOH A . E 3 HOH 104 278 104 HOH HOH A . E 3 HOH 105 279 105 HOH HOH A . E 3 HOH 106 280 106 HOH HOH A . E 3 HOH 107 281 107 HOH HOH A . E 3 HOH 108 282 108 HOH HOH A . E 3 HOH 109 283 109 HOH HOH A . E 3 HOH 110 284 110 HOH HOH A . E 3 HOH 111 285 111 HOH HOH A . E 3 HOH 112 286 112 HOH HOH A . E 3 HOH 113 287 113 HOH HOH A . E 3 HOH 114 288 114 HOH HOH A . E 3 HOH 115 289 115 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,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2520 ? 1 MORE -49 ? 1 'SSA (A^2)' 15640 ? # 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' 8_555 x-y,-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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 231 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 OE1 ? A GLU 128 ? A GLU 128 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 OE2 ? A GLU 130 ? A GLU 130 ? 1_555 135.9 ? 2 OE1 ? A GLU 128 ? A GLU 128 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 O ? E HOH . ? A HOH 182 ? 1_555 98.8 ? 3 OE2 ? A GLU 130 ? A GLU 130 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 O ? E HOH . ? A HOH 182 ? 1_555 70.1 ? 4 OE1 ? A GLU 128 ? A GLU 128 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 OE1 ? A GLU 130 ? A GLU 130 ? 1_555 97.5 ? 5 OE2 ? A GLU 130 ? A GLU 130 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 OE1 ? A GLU 130 ? A GLU 130 ? 1_555 50.7 ? 6 O ? E HOH . ? A HOH 182 ? 1_555 CD ? B CD . ? A CD 172 ? 1_555 OE1 ? A GLU 130 ? A GLU 130 ? 1_555 107.4 ? 7 OE1 ? A GLU 132 ? A GLU 132 ? 1_555 CD ? D CD . ? A CD 174 ? 1_555 O ? E HOH . ? A HOH 232 ? 1_555 85.7 ? 8 NE2 ? A HIS 141 ? A HIS 141 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 NE2 ? A HIS 145 ? A HIS 145 ? 1_555 102.7 ? 9 NE2 ? A HIS 141 ? A HIS 141 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 O ? E HOH . ? A HOH 177 ? 1_555 94.7 ? 10 NE2 ? A HIS 145 ? A HIS 145 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 O ? E HOH . ? A HOH 177 ? 1_555 85.1 ? 11 NE2 ? A HIS 141 ? A HIS 141 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 SG ? A CYS 99 ? A CYS 99 ? 1_555 121.2 ? 12 NE2 ? A HIS 145 ? A HIS 145 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 SG ? A CYS 99 ? A CYS 99 ? 1_555 100.3 ? 13 O ? E HOH . ? A HOH 177 ? 1_555 CD ? C CD . ? A CD 173 ? 1_555 SG ? A CYS 99 ? A CYS 99 ? 1_555 140.8 ? # 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 2009-06-30 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2016-10-12 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 3 'Structure model' repository Obsolete ? # _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 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 PHASES 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 113 ? ? OE2 A GLU 132 ? ? 1.98 2 1 OE1 A GLU 91 ? ? O A HOH 216 ? ? 2.02 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 CD _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 CD _pdbx_validate_symm_contact.auth_seq_id_1 172 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 209 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 8_545 _pdbx_validate_symm_contact.dist 2.09 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 68 ? ? CZ A ARG 68 ? ? NH1 A ARG 68 ? ? 117.27 120.30 -3.03 0.50 N 2 1 NE A ARG 116 ? ? CZ A ARG 116 ? ? NH2 A ARG 116 ? ? 115.76 120.30 -4.54 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 63 ? ? 179.67 155.14 2 1 GLU A 71 ? ? -43.54 24.61 3 1 SER A 168 ? ? -154.20 27.21 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 TYR _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 69 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 PRO _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 70 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -37.75 # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id LEU _pdbx_unobs_or_zero_occ_residues.auth_seq_id 171 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id LEU _pdbx_unobs_or_zero_occ_residues.label_seq_id 171 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CADMIUM ION' CD 3 water HOH #