data_3P9Z # _entry.id 3P9Z # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3P9Z RCSB RCSB062142 WWPDB D_1000062142 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id apc5866 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3P9Z _pdbx_database_status.recvd_initial_deposition_date 2010-10-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nocek, B.' 1 'Stein, A.' 2 'Chhor, G.' 3 'Fenske, R.J.' 4 'Buck, K.' 5 'Joachimiak, A.' 6 'Midwest Center for Structural Genomics (MCSG)' 7 # _citation.id primary _citation.title 'Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695' _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 'Nocek, B.' 1 primary 'Stein, A.' 2 primary 'Chhor, G.' 3 primary 'Fenske, R.J.' 4 primary 'Buck, K.' 5 primary 'Joachimiak, A.' 6 # _cell.entry_id 3P9Z _cell.length_a 55.407 _cell.length_b 57.676 _cell.length_c 74.624 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3P9Z _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 'Uroporphyrinogen III cosynthase (HemD)' 26309.197 1 ? ? ? ? 2 non-polymer syn 'MALONATE ION' 102.046 1 ? ? ? ? 3 water nat water 18.015 106 ? ? ? ? # _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 ;SNA(MSE)REIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNALIFTSKNAVFSLLETLKNSPKLK(MSE)LQNIPAYA LSEPTAKTLQDHHFKVAF(MSE)GEKAHGKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKH LTLSEQNALKPKEKSILIFTAISHAKAFLHYFEFLENYTAISIGNTTALYLQEQGIPSYIAKKPSLEACLELALSLRIKE C ; _entity_poly.pdbx_seq_one_letter_code_can ;SNAMREIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKT LQDHHFKVAFMGEKAHGKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSEQNALKPK EKSILIFTAISHAKAFLHYFEFLENYTAISIGNTTALYLQEQGIPSYIAKKPSLEACLELALSLRIKEC ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier apc5866 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 MSE n 1 5 ARG n 1 6 GLU n 1 7 ILE n 1 8 VAL n 1 9 TRP n 1 10 VAL n 1 11 HIS n 1 12 SER n 1 13 GLN n 1 14 ARG n 1 15 ILE n 1 16 ALA n 1 17 PRO n 1 18 TYR n 1 19 LYS n 1 20 THR n 1 21 LEU n 1 22 ILE n 1 23 LEU n 1 24 ASN n 1 25 GLU n 1 26 PHE n 1 27 CYS n 1 28 TYR n 1 29 TYR n 1 30 PRO n 1 31 LEU n 1 32 GLU n 1 33 LEU n 1 34 ASP n 1 35 PRO n 1 36 THR n 1 37 PRO n 1 38 PHE n 1 39 ASN n 1 40 ALA n 1 41 LEU n 1 42 ILE n 1 43 PHE n 1 44 THR n 1 45 SER n 1 46 LYS n 1 47 ASN n 1 48 ALA n 1 49 VAL n 1 50 PHE n 1 51 SER n 1 52 LEU n 1 53 LEU n 1 54 GLU n 1 55 THR n 1 56 LEU n 1 57 LYS n 1 58 ASN n 1 59 SER n 1 60 PRO n 1 61 LYS n 1 62 LEU n 1 63 LYS n 1 64 MSE n 1 65 LEU n 1 66 GLN n 1 67 ASN n 1 68 ILE n 1 69 PRO n 1 70 ALA n 1 71 TYR n 1 72 ALA n 1 73 LEU n 1 74 SER n 1 75 GLU n 1 76 PRO n 1 77 THR n 1 78 ALA n 1 79 LYS n 1 80 THR n 1 81 LEU n 1 82 GLN n 1 83 ASP n 1 84 HIS n 1 85 HIS n 1 86 PHE n 1 87 LYS n 1 88 VAL n 1 89 ALA n 1 90 PHE n 1 91 MSE n 1 92 GLY n 1 93 GLU n 1 94 LYS n 1 95 ALA n 1 96 HIS n 1 97 GLY n 1 98 LYS n 1 99 GLU n 1 100 PHE n 1 101 VAL n 1 102 GLN n 1 103 GLU n 1 104 ILE n 1 105 PHE n 1 106 PRO n 1 107 LEU n 1 108 LEU n 1 109 GLU n 1 110 LYS n 1 111 LYS n 1 112 SER n 1 113 VAL n 1 114 LEU n 1 115 TYR n 1 116 LEU n 1 117 ARG n 1 118 ALA n 1 119 LYS n 1 120 GLU n 1 121 ILE n 1 122 VAL n 1 123 SER n 1 124 SER n 1 125 LEU n 1 126 ASP n 1 127 THR n 1 128 ILE n 1 129 LEU n 1 130 LEU n 1 131 GLU n 1 132 HIS n 1 133 GLY n 1 134 ILE n 1 135 ASP n 1 136 PHE n 1 137 LYS n 1 138 GLN n 1 139 ALA n 1 140 VAL n 1 141 VAL n 1 142 TYR n 1 143 GLU n 1 144 ASN n 1 145 LYS n 1 146 LEU n 1 147 LYS n 1 148 HIS n 1 149 LEU n 1 150 THR n 1 151 LEU n 1 152 SER n 1 153 GLU n 1 154 GLN n 1 155 ASN n 1 156 ALA n 1 157 LEU n 1 158 LYS n 1 159 PRO n 1 160 LYS n 1 161 GLU n 1 162 LYS n 1 163 SER n 1 164 ILE n 1 165 LEU n 1 166 ILE n 1 167 PHE n 1 168 THR n 1 169 ALA n 1 170 ILE n 1 171 SER n 1 172 HIS n 1 173 ALA n 1 174 LYS n 1 175 ALA n 1 176 PHE n 1 177 LEU n 1 178 HIS n 1 179 TYR n 1 180 PHE n 1 181 GLU n 1 182 PHE n 1 183 LEU n 1 184 GLU n 1 185 ASN n 1 186 TYR n 1 187 THR n 1 188 ALA n 1 189 ILE n 1 190 SER n 1 191 ILE n 1 192 GLY n 1 193 ASN n 1 194 THR n 1 195 THR n 1 196 ALA n 1 197 LEU n 1 198 TYR n 1 199 LEU n 1 200 GLN n 1 201 GLU n 1 202 GLN n 1 203 GLY n 1 204 ILE n 1 205 PRO n 1 206 SER n 1 207 TYR n 1 208 ILE n 1 209 ALA n 1 210 LYS n 1 211 LYS n 1 212 PRO n 1 213 SER n 1 214 LEU n 1 215 GLU n 1 216 ALA n 1 217 CYS n 1 218 LEU n 1 219 GLU n 1 220 LEU n 1 221 ALA n 1 222 LEU n 1 223 SER n 1 224 LEU n 1 225 ARG n 1 226 ILE n 1 227 LYS n 1 228 GLU n 1 229 CYS 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 HP_1224 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Helicobacter pylori' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 210 _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 Bl21DE3 _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 pMCSG19B _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 O25822_HELPY _struct_ref.pdbx_db_accession O25822 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MREIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKTLQD HHFKVAFMGEKAHGKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSEQNALKPKEKS ILIFTAISHAKAFLHYFEFLENYTAISIGNTTALYLQEQGIPSYIAKKPSLEACLELALSLRIKEC ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3P9Z _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 229 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O25822 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 226 _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 226 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3P9Z SER A 1 ? UNP O25822 ? ? 'EXPRESSION TAG' -2 1 1 3P9Z ASN A 2 ? UNP O25822 ? ? 'EXPRESSION TAG' -1 2 1 3P9Z ALA A 3 ? UNP O25822 ? ? 'EXPRESSION TAG' 0 3 # 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 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 MLI non-polymer . 'MALONATE ION' ? 'C3 H2 O4 -2' 102.046 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 3P9Z _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.27 _exptl_crystal.density_percent_sol 45.72 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.0 _exptl_crystal_grow.pdbx_details '12% peg3350, 0.1 M Na malonate ph 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K' _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 315r' _diffrn_detector.pdbx_collection_date 2010-07-29 _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 'double crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9794 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9794 # _reflns.entry_id 3P9Z _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 35 _reflns.d_resolution_high 2.1 _reflns.number_obs 14570 _reflns.number_all 14570 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.11 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.18 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.56 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.8 _reflns_shell.pdbx_redundancy 6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1412 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3P9Z _refine.ls_number_reflns_obs 13733 _refine.ls_number_reflns_all 14570 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 35 _refine.ls_d_res_high 2.10 _refine.ls_percent_reflns_obs 99.22 _refine.ls_R_factor_obs 0.20418 _refine.ls_R_factor_all 0.210 _refine.ls_R_factor_R_work 0.20217 _refine.ls_R_factor_R_free 0.24108 _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 729 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.932 _refine.B_iso_mean 30.458 _refine.aniso_B[1][1] -0.04 _refine.aniso_B[2][2] -0.02 _refine.aniso_B[3][3] 0.07 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.187 _refine.overall_SU_ML 0.131 _refine.overall_SU_B 4.807 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_ESU_R 0.229 _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 1691 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 106 _refine_hist.number_atoms_total 1804 _refine_hist.d_res_high 2.10 _refine_hist.d_res_low 35 # 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 0.011 0.022 ? 1751 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.266 1.985 ? 2379 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.818 5.000 ? 217 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.909 24.328 ? 67 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.376 15.000 ? 311 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.443 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.088 0.200 ? 280 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.021 ? 1276 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.640 1.500 ? 1079 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.230 2.000 ? 1747 'X-RAY DIFFRACTION' ? r_scbond_it 2.098 3.000 ? 672 'X-RAY DIFFRACTION' ? r_scangle_it 3.522 4.500 ? 629 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.096 _refine_ls_shell.d_res_low 2.150 _refine_ls_shell.number_reflns_R_work 936 _refine_ls_shell.R_factor_R_work 0.259 _refine_ls_shell.percent_reflns_obs 94.96 _refine_ls_shell.R_factor_R_free 0.327 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 63 _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 3P9Z _struct.title 'Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695' _struct.pdbx_descriptor 'Uroporphyrinogen III cosynthase (HemD)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3P9Z _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text ;MCSG, PSI2, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, uroporphyrinogen-III synthetase, tetrapyrrole biosynthesis, heme, LIGASE ; # 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 SER A 45 ? LEU A 56 ? SER A 42 LEU A 53 1 ? 12 HELX_P HELX_P2 2 SER A 59 ? ASN A 67 ? SER A 56 ASN A 64 1 ? 9 HELX_P HELX_P3 3 SER A 74 ? HIS A 84 ? SER A 71 HIS A 81 1 ? 11 HELX_P HELX_P4 4 ILE A 104 ? GLU A 109 ? ILE A 101 GLU A 106 1 ? 6 HELX_P HELX_P5 5 SER A 124 ? HIS A 132 ? SER A 121 HIS A 129 1 ? 9 HELX_P HELX_P6 6 THR A 150 ? LYS A 158 ? THR A 147 LYS A 155 1 ? 9 HELX_P HELX_P7 7 ALA A 169 ? PHE A 180 ? ALA A 166 PHE A 177 1 ? 12 HELX_P HELX_P8 8 GLY A 192 ? GLN A 202 ? GLY A 189 GLN A 199 1 ? 11 HELX_P HELX_P9 9 SER A 213 ? LEU A 224 ? SER A 210 LEU A 221 1 ? 12 # _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 MSE 4 C ? ? ? 1_555 A ARG 5 N ? ? A MSE 1 A ARG 2 1_555 ? ? ? ? ? ? ? 1.330 ? covale2 covale ? ? A LYS 63 C ? ? ? 1_555 A MSE 64 N ? ? A LYS 60 A MSE 61 1_555 ? ? ? ? ? ? ? 1.342 ? covale3 covale ? ? A MSE 64 C ? ? ? 1_555 A LEU 65 N ? ? A MSE 61 A LEU 62 1_555 ? ? ? ? ? ? ? 1.336 ? covale4 covale ? ? A PHE 90 C ? ? ? 1_555 A MSE 91 N ? ? A PHE 87 A MSE 88 1_555 ? ? ? ? ? ? ? 1.334 ? covale5 covale ? ? A MSE 91 C ? ? ? 1_555 A GLY 92 N ? ? A MSE 88 A GLY 89 1_555 ? ? ? ? ? ? ? 1.319 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ALA _struct_mon_prot_cis.label_seq_id 16 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id ALA _struct_mon_prot_cis.auth_seq_id 13 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 17 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 14 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 2.51 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 5 ? # 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 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel B 1 2 ? anti-parallel B 2 3 ? parallel B 3 4 ? parallel B 4 5 ? 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 LYS A 19 ? LEU A 21 ? LYS A 16 LEU A 18 A 2 ILE A 7 ? VAL A 10 ? ILE A 4 VAL A 7 A 3 ILE A 164 ? PHE A 167 ? ILE A 161 PHE A 164 A 4 THR A 187 ? SER A 190 ? THR A 184 SER A 187 A 5 SER A 206 ? ILE A 208 ? SER A 203 ILE A 205 B 1 ASN A 24 ? TYR A 28 ? ASN A 21 TYR A 25 B 2 ASP A 135 ? LEU A 146 ? ASP A 132 LEU A 143 B 3 SER A 112 ? ALA A 118 ? SER A 109 ALA A 115 B 4 ALA A 40 ? PHE A 43 ? ALA A 37 PHE A 40 B 5 ALA A 70 ? ALA A 72 ? ALA A 67 ALA A 69 # 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 O LEU A 21 ? O LEU A 18 N TRP A 9 ? N TRP A 6 A 2 3 N VAL A 8 ? N VAL A 5 O ILE A 164 ? O ILE A 161 A 3 4 N PHE A 167 ? N PHE A 164 O ILE A 189 ? O ILE A 186 A 4 5 N SER A 190 ? N SER A 187 O TYR A 207 ? O TYR A 204 B 1 2 N GLU A 25 ? N GLU A 22 O LYS A 145 ? O LYS A 142 B 2 3 O LYS A 137 ? O LYS A 134 N TYR A 115 ? N TYR A 112 B 3 4 O LEU A 114 ? O LEU A 111 N ILE A 42 ? N ILE A 39 B 4 5 N LEU A 41 ? N LEU A 38 O TYR A 71 ? O TYR A 68 # _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 10 _struct_site.details 'BINDING SITE FOR RESIDUE MLI A 301' # 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 10 THR A 44 ? THR A 41 . ? 1_555 ? 2 AC1 10 TYR A 115 ? TYR A 112 . ? 1_555 ? 3 AC1 10 ARG A 117 ? ARG A 114 . ? 1_555 ? 4 AC1 10 GLU A 120 ? GLU A 117 . ? 1_555 ? 5 AC1 10 ILE A 121 ? ILE A 118 . ? 1_555 ? 6 AC1 10 VAL A 122 ? VAL A 119 . ? 1_555 ? 7 AC1 10 SER A 123 ? SER A 120 . ? 1_555 ? 8 AC1 10 SER A 124 ? SER A 121 . ? 1_555 ? 9 AC1 10 LEU A 125 ? LEU A 122 . ? 1_555 ? 10 AC1 10 HOH C . ? HOH A 259 . ? 1_555 ? # _database_PDB_matrix.entry_id 3P9Z _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 3P9Z _atom_sites.fract_transf_matrix[1][1] 0.018048 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017338 _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] 0.013401 _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 N O S SE # 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 SER 1 -2 ? ? ? A . n A 1 2 ASN 2 -1 ? ? ? A . n A 1 3 ALA 3 0 ? ? ? A . n A 1 4 MSE 4 1 1 MSE MSE A . n A 1 5 ARG 5 2 2 ARG ARG A . n A 1 6 GLU 6 3 3 GLU GLU A . n A 1 7 ILE 7 4 4 ILE ILE A . n A 1 8 VAL 8 5 5 VAL VAL A . n A 1 9 TRP 9 6 6 TRP TRP A . n A 1 10 VAL 10 7 7 VAL VAL A . n A 1 11 HIS 11 8 8 HIS HIS A . n A 1 12 SER 12 9 9 SER SER A . n A 1 13 GLN 13 10 10 GLN GLN A . n A 1 14 ARG 14 11 11 ARG ARG A . n A 1 15 ILE 15 12 12 ILE ILE A . n A 1 16 ALA 16 13 13 ALA ALA A . n A 1 17 PRO 17 14 14 PRO PRO A . n A 1 18 TYR 18 15 15 TYR TYR A . n A 1 19 LYS 19 16 16 LYS LYS A . n A 1 20 THR 20 17 17 THR THR A . n A 1 21 LEU 21 18 18 LEU LEU A . n A 1 22 ILE 22 19 19 ILE ILE A . n A 1 23 LEU 23 20 20 LEU LEU A . n A 1 24 ASN 24 21 21 ASN ASN A . n A 1 25 GLU 25 22 22 GLU GLU A . n A 1 26 PHE 26 23 23 PHE PHE A . n A 1 27 CYS 27 24 24 CYS CYS A . n A 1 28 TYR 28 25 25 TYR TYR A . n A 1 29 TYR 29 26 26 TYR TYR A . n A 1 30 PRO 30 27 27 PRO PRO A . n A 1 31 LEU 31 28 28 LEU LEU A . n A 1 32 GLU 32 29 29 GLU GLU A . n A 1 33 LEU 33 30 30 LEU LEU A . n A 1 34 ASP 34 31 31 ASP ASP A . n A 1 35 PRO 35 32 32 PRO PRO A . n A 1 36 THR 36 33 33 THR THR A . n A 1 37 PRO 37 34 34 PRO PRO A . n A 1 38 PHE 38 35 35 PHE PHE A . n A 1 39 ASN 39 36 36 ASN ASN A . n A 1 40 ALA 40 37 37 ALA ALA A . n A 1 41 LEU 41 38 38 LEU LEU A . n A 1 42 ILE 42 39 39 ILE ILE A . n A 1 43 PHE 43 40 40 PHE PHE A . n A 1 44 THR 44 41 41 THR THR A . n A 1 45 SER 45 42 42 SER SER A . n A 1 46 LYS 46 43 43 LYS LYS A . n A 1 47 ASN 47 44 44 ASN ASN A . n A 1 48 ALA 48 45 45 ALA ALA A . n A 1 49 VAL 49 46 46 VAL VAL A . n A 1 50 PHE 50 47 47 PHE PHE A . n A 1 51 SER 51 48 48 SER SER A . n A 1 52 LEU 52 49 49 LEU LEU A . n A 1 53 LEU 53 50 50 LEU LEU A . n A 1 54 GLU 54 51 51 GLU GLU A . n A 1 55 THR 55 52 52 THR THR A . n A 1 56 LEU 56 53 53 LEU LEU A . n A 1 57 LYS 57 54 54 LYS LYS A . n A 1 58 ASN 58 55 55 ASN ASN A . n A 1 59 SER 59 56 56 SER SER A . n A 1 60 PRO 60 57 57 PRO PRO A . n A 1 61 LYS 61 58 58 LYS LYS A . n A 1 62 LEU 62 59 59 LEU LEU A . n A 1 63 LYS 63 60 60 LYS LYS A . n A 1 64 MSE 64 61 61 MSE MSE A . n A 1 65 LEU 65 62 62 LEU LEU A . n A 1 66 GLN 66 63 63 GLN GLN A . n A 1 67 ASN 67 64 64 ASN ASN A . n A 1 68 ILE 68 65 65 ILE ILE A . n A 1 69 PRO 69 66 66 PRO PRO A . n A 1 70 ALA 70 67 67 ALA ALA A . n A 1 71 TYR 71 68 68 TYR TYR A . n A 1 72 ALA 72 69 69 ALA ALA A . n A 1 73 LEU 73 70 70 LEU LEU A . n A 1 74 SER 74 71 71 SER SER A . n A 1 75 GLU 75 72 72 GLU GLU A . n A 1 76 PRO 76 73 73 PRO PRO A . n A 1 77 THR 77 74 74 THR THR A . n A 1 78 ALA 78 75 75 ALA ALA A . n A 1 79 LYS 79 76 76 LYS LYS A . n A 1 80 THR 80 77 77 THR THR A . n A 1 81 LEU 81 78 78 LEU LEU A . n A 1 82 GLN 82 79 79 GLN GLN A . n A 1 83 ASP 83 80 80 ASP ASP A . n A 1 84 HIS 84 81 81 HIS HIS A . n A 1 85 HIS 85 82 82 HIS HIS A . n A 1 86 PHE 86 83 83 PHE PHE A . n A 1 87 LYS 87 84 84 LYS LYS A . n A 1 88 VAL 88 85 85 VAL VAL A . n A 1 89 ALA 89 86 86 ALA ALA A . n A 1 90 PHE 90 87 87 PHE PHE A . n A 1 91 MSE 91 88 88 MSE MSE A . n A 1 92 GLY 92 89 89 GLY GLY A . n A 1 93 GLU 93 90 90 GLU GLU A . n A 1 94 LYS 94 91 ? ? ? A . n A 1 95 ALA 95 92 ? ? ? A . n A 1 96 HIS 96 93 ? ? ? A . n A 1 97 GLY 97 94 ? ? ? A . n A 1 98 LYS 98 95 ? ? ? A . n A 1 99 GLU 99 96 ? ? ? A . n A 1 100 PHE 100 97 ? ? ? A . n A 1 101 VAL 101 98 ? ? ? A . n A 1 102 GLN 102 99 ? ? ? A . n A 1 103 GLU 103 100 100 GLU GLU A . n A 1 104 ILE 104 101 101 ILE ILE A . n A 1 105 PHE 105 102 102 PHE PHE A . n A 1 106 PRO 106 103 103 PRO PRO A . n A 1 107 LEU 107 104 104 LEU LEU A . n A 1 108 LEU 108 105 105 LEU LEU A . n A 1 109 GLU 109 106 106 GLU GLU A . n A 1 110 LYS 110 107 107 LYS LYS A . n A 1 111 LYS 111 108 108 LYS LYS A . n A 1 112 SER 112 109 109 SER SER A . n A 1 113 VAL 113 110 110 VAL VAL A . n A 1 114 LEU 114 111 111 LEU LEU A . n A 1 115 TYR 115 112 112 TYR TYR A . n A 1 116 LEU 116 113 113 LEU LEU A . n A 1 117 ARG 117 114 114 ARG ARG A . n A 1 118 ALA 118 115 115 ALA ALA A . n A 1 119 LYS 119 116 116 LYS LYS A . n A 1 120 GLU 120 117 117 GLU GLU A . n A 1 121 ILE 121 118 118 ILE ILE A . n A 1 122 VAL 122 119 119 VAL VAL A . n A 1 123 SER 123 120 120 SER SER A . n A 1 124 SER 124 121 121 SER SER A . n A 1 125 LEU 125 122 122 LEU LEU A . n A 1 126 ASP 126 123 123 ASP ASP A . n A 1 127 THR 127 124 124 THR THR A . n A 1 128 ILE 128 125 125 ILE ILE A . n A 1 129 LEU 129 126 126 LEU LEU A . n A 1 130 LEU 130 127 127 LEU LEU A . n A 1 131 GLU 131 128 128 GLU GLU A . n A 1 132 HIS 132 129 129 HIS HIS A . n A 1 133 GLY 133 130 130 GLY GLY A . n A 1 134 ILE 134 131 131 ILE ILE A . n A 1 135 ASP 135 132 132 ASP ASP A . n A 1 136 PHE 136 133 133 PHE PHE A . n A 1 137 LYS 137 134 134 LYS LYS A . n A 1 138 GLN 138 135 135 GLN GLN A . n A 1 139 ALA 139 136 136 ALA ALA A . n A 1 140 VAL 140 137 137 VAL VAL A . n A 1 141 VAL 141 138 138 VAL VAL A . n A 1 142 TYR 142 139 139 TYR TYR A . n A 1 143 GLU 143 140 140 GLU GLU A . n A 1 144 ASN 144 141 141 ASN ASN A . n A 1 145 LYS 145 142 142 LYS LYS A . n A 1 146 LEU 146 143 143 LEU LEU A . n A 1 147 LYS 147 144 144 LYS LYS A . n A 1 148 HIS 148 145 145 HIS HIS A . n A 1 149 LEU 149 146 146 LEU LEU A . n A 1 150 THR 150 147 147 THR THR A . n A 1 151 LEU 151 148 148 LEU LEU A . n A 1 152 SER 152 149 149 SER SER A . n A 1 153 GLU 153 150 150 GLU GLU A . n A 1 154 GLN 154 151 151 GLN GLN A . n A 1 155 ASN 155 152 152 ASN ASN A . n A 1 156 ALA 156 153 153 ALA ALA A . n A 1 157 LEU 157 154 154 LEU LEU A . n A 1 158 LYS 158 155 155 LYS LYS A . n A 1 159 PRO 159 156 156 PRO PRO A . n A 1 160 LYS 160 157 157 LYS LYS A . n A 1 161 GLU 161 158 158 GLU GLU A . n A 1 162 LYS 162 159 159 LYS LYS A . n A 1 163 SER 163 160 160 SER SER A . n A 1 164 ILE 164 161 161 ILE ILE A . n A 1 165 LEU 165 162 162 LEU LEU A . n A 1 166 ILE 166 163 163 ILE ILE A . n A 1 167 PHE 167 164 164 PHE PHE A . n A 1 168 THR 168 165 165 THR THR A . n A 1 169 ALA 169 166 166 ALA ALA A . n A 1 170 ILE 170 167 167 ILE ILE A . n A 1 171 SER 171 168 168 SER SER A . n A 1 172 HIS 172 169 169 HIS HIS A . n A 1 173 ALA 173 170 170 ALA ALA A . n A 1 174 LYS 174 171 171 LYS LYS A . n A 1 175 ALA 175 172 172 ALA ALA A . n A 1 176 PHE 176 173 173 PHE PHE A . n A 1 177 LEU 177 174 174 LEU LEU A . n A 1 178 HIS 178 175 175 HIS HIS A . n A 1 179 TYR 179 176 176 TYR TYR A . n A 1 180 PHE 180 177 177 PHE PHE A . n A 1 181 GLU 181 178 178 GLU GLU A . n A 1 182 PHE 182 179 179 PHE PHE A . n A 1 183 LEU 183 180 180 LEU LEU A . n A 1 184 GLU 184 181 181 GLU GLU A . n A 1 185 ASN 185 182 182 ASN ASN A . n A 1 186 TYR 186 183 183 TYR TYR A . n A 1 187 THR 187 184 184 THR THR A . n A 1 188 ALA 188 185 185 ALA ALA A . n A 1 189 ILE 189 186 186 ILE ILE A . n A 1 190 SER 190 187 187 SER SER A . n A 1 191 ILE 191 188 188 ILE ILE A . n A 1 192 GLY 192 189 189 GLY GLY A . n A 1 193 ASN 193 190 190 ASN ASN A . n A 1 194 THR 194 191 191 THR THR A . n A 1 195 THR 195 192 192 THR THR A . n A 1 196 ALA 196 193 193 ALA ALA A . n A 1 197 LEU 197 194 194 LEU LEU A . n A 1 198 TYR 198 195 195 TYR TYR A . n A 1 199 LEU 199 196 196 LEU LEU A . n A 1 200 GLN 200 197 197 GLN GLN A . n A 1 201 GLU 201 198 198 GLU GLU A . n A 1 202 GLN 202 199 199 GLN GLN A . n A 1 203 GLY 203 200 200 GLY GLY A . n A 1 204 ILE 204 201 201 ILE ILE A . n A 1 205 PRO 205 202 202 PRO PRO A . n A 1 206 SER 206 203 203 SER SER A . n A 1 207 TYR 207 204 204 TYR TYR A . n A 1 208 ILE 208 205 205 ILE ILE A . n A 1 209 ALA 209 206 206 ALA ALA A . n A 1 210 LYS 210 207 207 LYS LYS A . n A 1 211 LYS 211 208 208 LYS LYS A . n A 1 212 PRO 212 209 209 PRO PRO A . n A 1 213 SER 213 210 210 SER SER A . n A 1 214 LEU 214 211 211 LEU LEU A . n A 1 215 GLU 215 212 212 GLU GLU A . n A 1 216 ALA 216 213 213 ALA ALA A . n A 1 217 CYS 217 214 214 CYS CYS A . n A 1 218 LEU 218 215 215 LEU LEU A . n A 1 219 GLU 219 216 216 GLU GLU A . n A 1 220 LEU 220 217 217 LEU LEU A . n A 1 221 ALA 221 218 218 ALA ALA A . n A 1 222 LEU 222 219 219 LEU LEU A . n A 1 223 SER 223 220 220 SER SER A . n A 1 224 LEU 224 221 221 LEU LEU A . n A 1 225 ARG 225 222 222 ARG ARG A . n A 1 226 ILE 226 223 ? ? ? A . n A 1 227 LYS 227 224 ? ? ? A . n A 1 228 GLU 228 225 ? ? ? A . n A 1 229 CYS 229 226 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Midwest Center for Structural Genomics' _pdbx_SG_project.initial_of_center MCSG # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 4 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 64 A MSE 61 ? MET SELENOMETHIONINE 3 A MSE 91 A MSE 88 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_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 2010-11-03 2 'Structure model' 1 1 2011-07-13 # _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 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SBC-Collect 'data collection' . ? 1 Auto-Rickshaw phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 HKL-3000 'data reduction' . ? 4 HKL-3000 'data scaling' . ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 55 ? ? 61.83 -0.77 2 1 VAL A 119 ? ? -116.92 -75.56 3 1 SER A 121 ? ? 34.67 57.39 # 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 Y 1 A GLU 29 ? CG ? A GLU 32 CG 2 1 Y 1 A GLU 29 ? CD ? A GLU 32 CD 3 1 Y 1 A GLU 29 ? OE1 ? A GLU 32 OE1 4 1 Y 1 A GLU 29 ? OE2 ? A GLU 32 OE2 5 1 Y 1 A LEU 30 ? CG ? A LEU 33 CG 6 1 Y 1 A LEU 30 ? CD1 ? A LEU 33 CD1 7 1 Y 1 A LEU 30 ? CD2 ? A LEU 33 CD2 8 1 Y 1 A LYS 54 ? CG ? A LYS 57 CG 9 1 Y 1 A LYS 54 ? CD ? A LYS 57 CD 10 1 Y 1 A LYS 54 ? CE ? A LYS 57 CE 11 1 Y 1 A LYS 54 ? NZ ? A LYS 57 NZ 12 1 Y 1 A ASN 55 ? CG ? A ASN 58 CG 13 1 Y 1 A ASN 55 ? OD1 ? A ASN 58 OD1 14 1 Y 1 A ASN 55 ? ND2 ? A ASN 58 ND2 15 1 Y 1 A GLU 72 ? CG ? A GLU 75 CG 16 1 Y 1 A GLU 72 ? CD ? A GLU 75 CD 17 1 Y 1 A GLU 72 ? OE1 ? A GLU 75 OE1 18 1 Y 1 A GLU 72 ? OE2 ? A GLU 75 OE2 19 1 Y 1 A GLU 106 ? CG ? A GLU 109 CG 20 1 Y 1 A GLU 106 ? CD ? A GLU 109 CD 21 1 Y 1 A GLU 106 ? OE1 ? A GLU 109 OE1 22 1 Y 1 A GLU 106 ? OE2 ? A GLU 109 OE2 23 1 Y 1 A LYS 157 ? CG ? A LYS 160 CG 24 1 Y 1 A LYS 157 ? CD ? A LYS 160 CD 25 1 Y 1 A LYS 157 ? CE ? A LYS 160 CE 26 1 Y 1 A LYS 157 ? NZ ? A LYS 160 NZ 27 1 Y 1 A GLU 181 ? CG ? A GLU 184 CG 28 1 Y 1 A GLU 181 ? CD ? A GLU 184 CD 29 1 Y 1 A GLU 181 ? OE1 ? A GLU 184 OE1 30 1 Y 1 A GLU 181 ? OE2 ? A GLU 184 OE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A SER -2 ? A SER 1 2 1 Y 1 A ASN -1 ? A ASN 2 3 1 Y 1 A ALA 0 ? A ALA 3 4 1 Y 1 A LYS 91 ? A LYS 94 5 1 Y 1 A ALA 92 ? A ALA 95 6 1 Y 1 A HIS 93 ? A HIS 96 7 1 Y 1 A GLY 94 ? A GLY 97 8 1 Y 1 A LYS 95 ? A LYS 98 9 1 Y 1 A GLU 96 ? A GLU 99 10 1 Y 1 A PHE 97 ? A PHE 100 11 1 Y 1 A VAL 98 ? A VAL 101 12 1 Y 1 A GLN 99 ? A GLN 102 13 1 Y 1 A ILE 223 ? A ILE 226 14 1 Y 1 A LYS 224 ? A LYS 227 15 1 Y 1 A GLU 225 ? A GLU 228 16 1 Y 1 A CYS 226 ? A CYS 229 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MALONATE ION' MLI 3 water HOH # 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 MLI 1 301 301 MLI MLI A . C 3 HOH 1 227 227 HOH HOH A . C 3 HOH 2 228 228 HOH HOH A . C 3 HOH 3 229 229 HOH HOH A . C 3 HOH 4 230 230 HOH HOH A . C 3 HOH 5 231 231 HOH HOH A . C 3 HOH 6 232 232 HOH HOH A . C 3 HOH 7 233 233 HOH HOH A . C 3 HOH 8 234 234 HOH HOH A . C 3 HOH 9 235 235 HOH HOH A . C 3 HOH 10 236 236 HOH HOH A . C 3 HOH 11 237 237 HOH HOH A . C 3 HOH 12 238 238 HOH HOH A . C 3 HOH 13 239 239 HOH HOH A . C 3 HOH 14 240 240 HOH HOH A . C 3 HOH 15 241 241 HOH HOH A . C 3 HOH 16 242 242 HOH HOH A . C 3 HOH 17 243 243 HOH HOH A . C 3 HOH 18 244 244 HOH HOH A . C 3 HOH 19 245 245 HOH HOH A . C 3 HOH 20 246 246 HOH HOH A . C 3 HOH 21 247 247 HOH HOH A . C 3 HOH 22 248 248 HOH HOH A . C 3 HOH 23 249 249 HOH HOH A . C 3 HOH 24 250 250 HOH HOH A . C 3 HOH 25 251 251 HOH HOH A . C 3 HOH 26 252 252 HOH HOH A . C 3 HOH 27 253 253 HOH HOH A . C 3 HOH 28 254 254 HOH HOH A . C 3 HOH 29 255 255 HOH HOH A . C 3 HOH 30 256 256 HOH HOH A . C 3 HOH 31 257 257 HOH HOH A . C 3 HOH 32 258 258 HOH HOH A . C 3 HOH 33 259 259 HOH HOH A . C 3 HOH 34 260 260 HOH HOH A . C 3 HOH 35 261 261 HOH HOH A . C 3 HOH 36 262 262 HOH HOH A . C 3 HOH 37 263 263 HOH HOH A . C 3 HOH 38 264 264 HOH HOH A . C 3 HOH 39 265 265 HOH HOH A . C 3 HOH 40 266 266 HOH HOH A . C 3 HOH 41 267 267 HOH HOH A . C 3 HOH 42 268 268 HOH HOH A . C 3 HOH 43 269 269 HOH HOH A . C 3 HOH 44 270 270 HOH HOH A . C 3 HOH 45 271 271 HOH HOH A . C 3 HOH 46 272 272 HOH HOH A . C 3 HOH 47 273 273 HOH HOH A . C 3 HOH 48 274 274 HOH HOH A . C 3 HOH 49 275 275 HOH HOH A . C 3 HOH 50 276 276 HOH HOH A . C 3 HOH 51 277 277 HOH HOH A . C 3 HOH 52 278 278 HOH HOH A . C 3 HOH 53 279 279 HOH HOH A . C 3 HOH 54 280 280 HOH HOH A . C 3 HOH 55 281 281 HOH HOH A . C 3 HOH 56 282 282 HOH HOH A . C 3 HOH 57 283 283 HOH HOH A . C 3 HOH 58 284 284 HOH HOH A . C 3 HOH 59 285 285 HOH HOH A . C 3 HOH 60 286 286 HOH HOH A . C 3 HOH 61 287 287 HOH HOH A . C 3 HOH 62 288 288 HOH HOH A . C 3 HOH 63 289 289 HOH HOH A . C 3 HOH 64 290 290 HOH HOH A . C 3 HOH 65 291 291 HOH HOH A . C 3 HOH 66 292 292 HOH HOH A . C 3 HOH 67 293 293 HOH HOH A . C 3 HOH 68 294 294 HOH HOH A . C 3 HOH 69 295 295 HOH HOH A . C 3 HOH 70 296 296 HOH HOH A . C 3 HOH 71 297 297 HOH HOH A . C 3 HOH 72 298 298 HOH HOH A . C 3 HOH 73 299 299 HOH HOH A . C 3 HOH 74 300 300 HOH HOH A . C 3 HOH 75 302 302 HOH HOH A . C 3 HOH 76 303 303 HOH HOH A . C 3 HOH 77 304 304 HOH HOH A . C 3 HOH 78 305 305 HOH HOH A . C 3 HOH 79 306 306 HOH HOH A . C 3 HOH 80 307 307 HOH HOH A . C 3 HOH 81 308 308 HOH HOH A . C 3 HOH 82 309 309 HOH HOH A . C 3 HOH 83 310 310 HOH HOH A . C 3 HOH 84 311 311 HOH HOH A . C 3 HOH 85 312 312 HOH HOH A . C 3 HOH 86 313 313 HOH HOH A . C 3 HOH 87 314 314 HOH HOH A . C 3 HOH 88 315 315 HOH HOH A . C 3 HOH 89 316 316 HOH HOH A . C 3 HOH 90 317 317 HOH HOH A . C 3 HOH 91 318 318 HOH HOH A . C 3 HOH 92 319 319 HOH HOH A . C 3 HOH 93 320 320 HOH HOH A . C 3 HOH 94 321 321 HOH HOH A . C 3 HOH 95 322 322 HOH HOH A . C 3 HOH 96 323 323 HOH HOH A . C 3 HOH 97 324 324 HOH HOH A . C 3 HOH 98 325 325 HOH HOH A . C 3 HOH 99 326 326 HOH HOH A . C 3 HOH 100 327 327 HOH HOH A . C 3 HOH 101 328 328 HOH HOH A . C 3 HOH 102 329 329 HOH HOH A . C 3 HOH 103 330 330 HOH HOH A . C 3 HOH 104 331 331 HOH HOH A . C 3 HOH 105 332 332 HOH HOH A . C 3 HOH 106 333 333 HOH HOH A . #