data_2TDT # _entry.id 2TDT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2TDT pdb_00002tdt 10.2210/pdb2tdt/pdb WWPDB D_1000178668 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2TDT _pdbx_database_status.recvd_initial_deposition_date 1998-05-05 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Beaman, T.W.' 1 'Blanchard, J.S.' 2 'Roderick, S.L.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.' Biochemistry 37 10363 10369 1998 BICHAW US 0006-2960 0033 ? 9671504 10.1021/bi980759b 1 'Three-Dimensional Structure of Tetrahydrodipicolinate N-Succinyltransferase' Biochemistry 36 489 ? 1997 BICHAW US 0006-2960 0033 ? ? ? 2 'Crystallization and Preliminary Crystallographic Analysis of Tetrahydrodipicolinate-N-Succinyltransferase' Proteins 26 115 ? 1996 PSFGEY US 0887-3585 0867 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Beaman, T.W.' 1 ? primary 'Blanchard, J.S.' 2 ? primary 'Roderick, S.L.' 3 ? 1 'Beaman, T.W.' 4 ? 1 'Binder, D.A.' 5 ? 1 'Blanchard, J.S.' 6 ? 1 'Roderick, S.L.' 7 ? 2 'Binder, D.A.' 8 ? 2 'Blanchard, J.S.' 9 ? 2 'Roderick, S.L.' 10 ? # _cell.entry_id 2TDT _cell.length_a 95.710 _cell.length_b 95.710 _cell.length_c 72.790 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2TDT _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 # 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 'TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE' 29918.990 1 2.3.1.117 ? ? ? 2 non-polymer syn 'COENZYME A' 767.534 1 ? ? ? ? 3 non-polymer syn '(2S)-2-aminoheptanedioic acid' 175.182 1 ? ? ? ? 4 water nat water 18.015 85 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name DAPD # _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 ;MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAET RYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSG GVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS KDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID ; _entity_poly.pdbx_seq_one_letter_code_can ;MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAET RYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSG GVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS KDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID ; _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 GLN n 1 3 GLN n 1 4 LEU n 1 5 GLN n 1 6 ASN n 1 7 VAL n 1 8 ILE n 1 9 GLU n 1 10 SER n 1 11 ALA n 1 12 PHE n 1 13 GLU n 1 14 ARG n 1 15 ARG n 1 16 ALA n 1 17 ASP n 1 18 ILE n 1 19 THR n 1 20 PRO n 1 21 ALA n 1 22 ASN n 1 23 VAL n 1 24 ASP n 1 25 THR n 1 26 VAL n 1 27 THR n 1 28 ARG n 1 29 GLU n 1 30 ALA n 1 31 VAL n 1 32 ASN n 1 33 GLN n 1 34 VAL n 1 35 ILE n 1 36 GLY n 1 37 LEU n 1 38 LEU n 1 39 ASP n 1 40 SER n 1 41 GLY n 1 42 ALA n 1 43 LEU n 1 44 ARG n 1 45 VAL n 1 46 ALA n 1 47 GLU n 1 48 LYS n 1 49 ILE n 1 50 ASP n 1 51 GLY n 1 52 GLN n 1 53 TRP n 1 54 VAL n 1 55 THR n 1 56 HIS n 1 57 GLN n 1 58 TRP n 1 59 LEU n 1 60 LYS n 1 61 LYS n 1 62 ALA n 1 63 VAL n 1 64 LEU n 1 65 LEU n 1 66 SER n 1 67 PHE n 1 68 ARG n 1 69 ILE n 1 70 ASN n 1 71 ASP n 1 72 ASN n 1 73 LYS n 1 74 VAL n 1 75 MET n 1 76 ASP n 1 77 GLY n 1 78 ALA n 1 79 GLU n 1 80 THR n 1 81 ARG n 1 82 TYR n 1 83 TYR n 1 84 ASP n 1 85 LYS n 1 86 VAL n 1 87 PRO n 1 88 MET n 1 89 LYS n 1 90 PHE n 1 91 ALA n 1 92 ASP n 1 93 TYR n 1 94 ASP n 1 95 GLU n 1 96 ALA n 1 97 ARG n 1 98 PHE n 1 99 GLN n 1 100 LYS n 1 101 GLU n 1 102 GLY n 1 103 PHE n 1 104 ARG n 1 105 VAL n 1 106 VAL n 1 107 PRO n 1 108 PRO n 1 109 ALA n 1 110 THR n 1 111 VAL n 1 112 ARG n 1 113 GLN n 1 114 GLY n 1 115 ALA n 1 116 PHE n 1 117 ILE n 1 118 ALA n 1 119 ARG n 1 120 ASN n 1 121 THR n 1 122 VAL n 1 123 LEU n 1 124 MET n 1 125 PRO n 1 126 SER n 1 127 TYR n 1 128 VAL n 1 129 ASN n 1 130 ILE n 1 131 GLY n 1 132 ALA n 1 133 TYR n 1 134 VAL n 1 135 ASP n 1 136 GLU n 1 137 GLY n 1 138 THR n 1 139 MET n 1 140 VAL n 1 141 ASP n 1 142 THR n 1 143 TRP n 1 144 ALA n 1 145 THR n 1 146 VAL n 1 147 GLY n 1 148 SER n 1 149 CYS n 1 150 ALA n 1 151 GLN n 1 152 ILE n 1 153 GLY n 1 154 LYS n 1 155 ASN n 1 156 VAL n 1 157 HIS n 1 158 LEU n 1 159 SER n 1 160 GLY n 1 161 GLY n 1 162 VAL n 1 163 GLY n 1 164 ILE n 1 165 GLY n 1 166 GLY n 1 167 VAL n 1 168 LEU n 1 169 GLU n 1 170 PRO n 1 171 LEU n 1 172 GLN n 1 173 ALA n 1 174 ASN n 1 175 PRO n 1 176 THR n 1 177 ILE n 1 178 ILE n 1 179 GLU n 1 180 ASP n 1 181 ASN n 1 182 CYS n 1 183 PHE n 1 184 ILE n 1 185 GLY n 1 186 ALA n 1 187 ARG n 1 188 SER n 1 189 GLU n 1 190 VAL n 1 191 VAL n 1 192 GLU n 1 193 GLY n 1 194 VAL n 1 195 ILE n 1 196 VAL n 1 197 GLU n 1 198 GLU n 1 199 GLY n 1 200 SER n 1 201 VAL n 1 202 ILE n 1 203 SER n 1 204 MET n 1 205 GLY n 1 206 VAL n 1 207 TYR n 1 208 LEU n 1 209 GLY n 1 210 GLN n 1 211 SER n 1 212 THR n 1 213 ARG n 1 214 ILE n 1 215 TYR n 1 216 ASP n 1 217 ARG n 1 218 GLU n 1 219 THR n 1 220 GLY n 1 221 GLU n 1 222 ILE n 1 223 HIS n 1 224 TYR n 1 225 GLY n 1 226 ARG n 1 227 VAL n 1 228 PRO n 1 229 ALA n 1 230 GLY n 1 231 SER n 1 232 VAL n 1 233 VAL n 1 234 VAL n 1 235 SER n 1 236 GLY n 1 237 ASN n 1 238 LEU n 1 239 PRO n 1 240 SER n 1 241 LYS n 1 242 ASP n 1 243 GLY n 1 244 SER n 1 245 TYR n 1 246 SER n 1 247 LEU n 1 248 TYR n 1 249 CYS n 1 250 ALA n 1 251 VAL n 1 252 ILE n 1 253 VAL n 1 254 LYS n 1 255 LYS n 1 256 VAL n 1 257 ASP n 1 258 ALA n 1 259 LYS n 1 260 THR n 1 261 ARG n 1 262 GLY n 1 263 LYS n 1 264 VAL n 1 265 GLY n 1 266 ILE n 1 267 ASN n 1 268 GLU n 1 269 LEU n 1 270 LEU n 1 271 ARG n 1 272 THR n 1 273 ILE n 1 274 ASP 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 Mycobacterium _entity_src_gen.pdbx_gene_src_gene DAPD _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 'Mycobacterium bovis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1765 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line BL21 _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 Escherichia _entity_src_gen.pdbx_host_org_gene DAPD _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21 (DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PET3A _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code DAPD_MYCBO _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession P56220 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ;MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAET RYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSG GVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS KDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID ; _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2TDT _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 274 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P56220 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 274 _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 274 # 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 COA non-polymer . 'COENZYME A' ? 'C21 H36 N7 O16 P3 S' 767.534 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 NPI 'L-peptide linking' n '(2S)-2-aminoheptanedioic acid' 'L-2-AMINOPIMELIC ACID' 'C7 H13 N O4' 175.182 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 2TDT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 43 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.4 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;10-13 % (W/V) POLYETHYLENE GLYCOL 4000 94 MM MES, PH 6.4 94 MM AMMONIUM SULFATE 4.7 (V/V) 2-PROPANOL 16 MM (D,L)-2-AMINOPIMELATE 2.5 MM COENZYME A ; # _diffrn.id 1 _diffrn.ambient_temp 295 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type SIEMENS _diffrn_detector.pdbx_collection_date 1997-08 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'GRAPHITE(002)' _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RUH2R' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 2TDT _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.0 _reflns.number_obs 44276 _reflns.number_all ? _reflns.percent_possible_obs 98.1 _reflns.pdbx_Rmerge_I_obs 0.0470000 _reflns.pdbx_Rsym_value 0.0470000 _reflns.pdbx_netI_over_sigmaI 22.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.7 _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.1 _reflns_shell.percent_possible_all 98.1 _reflns_shell.Rmerge_I_obs 0.2150000 _reflns_shell.pdbx_Rsym_value 0.2150000 _reflns_shell.meanI_over_sigI_obs 3.4 _reflns_shell.pdbx_redundancy 1.3 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2TDT _refine.ls_number_reflns_obs 16215 _refine.ls_number_reflns_all 16215 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 99.0 _refine.ls_d_res_high 2.0 _refine.ls_percent_reflns_obs 98.1 _refine.ls_R_factor_obs 0.1710000 _refine.ls_R_factor_all 0.1710000 _refine.ls_R_factor_R_work 0.1690000 _refine.ls_R_factor_R_free 0.2400000 _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 813 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol 0.61 _refine.solvent_model_param_bsol 205 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1TDT' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model 'TNT BCORREL' _refine.pdbx_stereochemistry_target_values 'TNT PROTGEO' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details SHELLS _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 2075 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 60 _refine_hist.number_atoms_solvent 85 _refine_hist.number_atoms_total 2220 _refine_hist.d_res_high 2.0 _refine_hist.d_res_low 99.0 # 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 t_bond_d 0.023 ? 0.8 2170 'X-RAY DIFFRACTION' ? t_angle_deg 1.94 ? 1.3 2936 'X-RAY DIFFRACTION' ? t_dihedral_angle_d 23.9 ? 0.0 1279 'X-RAY DIFFRACTION' ? t_incorr_chiral_ct 0 ? ? ? 'X-RAY DIFFRACTION' ? t_pseud_angle ? ? ? ? 'X-RAY DIFFRACTION' ? t_trig_c_planes 0.011 ? 2 53 'X-RAY DIFFRACTION' ? t_gen_planes 0.017 ? 5.0 315 'X-RAY DIFFRACTION' ? t_it 5.22 ? 3.00 4278 'X-RAY DIFFRACTION' ? t_nbd 0.025 ? 10.0 25 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 2TDT _pdbx_refine.R_factor_all_no_cutoff 0.1710000 _pdbx_refine.R_factor_obs_no_cutoff 0.1690000 _pdbx_refine.free_R_factor_no_cutoff 0.2460000 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 813 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 2TDT _struct.title 'COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINOPIMELATE AND COENZYME A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2TDT _struct_keywords.pdbx_keywords ACYLTRANSFERASE _struct_keywords.text 'ACYLTRANSFERASE, LYSINE BIOSYNTHESIS' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _struct_biol.id 1 # 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 GLN A 2 ? ASP A 17 ? GLN A 2 ASP A 17 1 ? 16 HELX_P HELX_P2 2 THR A 25 ? SER A 40 ? THR A 25 SER A 40 1 ? 16 HELX_P HELX_P3 3 GLN A 57 ? ILE A 69 ? GLN A 57 ILE A 69 1 ? 13 HELX_P HELX_P4 4 LYS A 89 ? ALA A 91 ? LYS A 89 ALA A 91 5 ? 3 HELX_P HELX_P5 5 GLU A 95 ? GLU A 101 ? GLU A 95 GLU A 101 1 ? 7 HELX_P HELX_P6 6 ALA A 258 ? VAL A 264 ? ALA A 258 VAL A 264 1 ? 7 HELX_P HELX_P7 7 GLU A 268 ? LEU A 270 ? GLU A 268 LEU A 270 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 PRO 107 A . ? PRO 107 A PRO 108 A ? PRO 108 A 1 3.10 2 GLU 169 A . ? GLU 169 A PRO 170 A ? PRO 170 A 1 -1.37 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? B ? 2 ? C ? 2 ? D ? 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 B 1 2 ? anti-parallel C 1 2 ? parallel D 1 2 ? parallel D 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 ALA A 46 ? ILE A 49 ? ALA A 46 ILE A 49 A 2 GLN A 52 ? THR A 55 ? GLN A 52 THR A 55 B 1 LYS A 73 ? ASP A 76 ? LYS A 73 ASP A 76 B 2 ARG A 81 ? ASP A 84 ? ARG A 81 ASP A 84 C 1 SER A 126 ? VAL A 128 ? SER A 126 VAL A 128 C 2 ALA A 144 ? VAL A 146 ? ALA A 144 VAL A 146 D 1 ILE A 214 ? ASP A 216 ? ILE A 214 ASP A 216 D 2 SER A 246 ? LYS A 255 ? SER A 246 LYS A 255 D 3 SER A 231 ? PRO A 239 ? SER A 231 PRO A 239 # 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 GLU A 47 ? O GLU A 47 N VAL A 54 ? N VAL A 54 B 1 2 O LYS A 73 ? O LYS A 73 N ASP A 84 ? N ASP A 84 C 1 2 O TYR A 127 ? O TYR A 127 N ALA A 144 ? N ALA A 144 D 1 2 O TYR A 215 ? O TYR A 215 N ALA A 250 ? N ALA A 250 D 2 3 O LEU A 247 ? O LEU A 247 N LEU A 238 ? N LEU A 238 # 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 A COA 280 ? 22 'BINDING SITE FOR RESIDUE COA A 280' AC2 Software A NPI 281 ? 13 'BINDING SITE FOR RESIDUE NPI A 281' # 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 22 ASP A 141 ? ASP A 141 . ? 1_555 ? 2 AC1 22 SER A 159 ? SER A 159 . ? 1_555 ? 3 AC1 22 GLY A 160 ? GLY A 160 . ? 1_555 ? 4 AC1 22 GLY A 185 ? GLY A 185 . ? 1_555 ? 5 AC1 22 ALA A 186 ? ALA A 186 . ? 1_555 ? 6 AC1 22 GLU A 192 ? GLU A 192 . ? 3_555 ? 7 AC1 22 SER A 203 ? SER A 203 . ? 1_555 ? 8 AC1 22 MET A 204 ? MET A 204 . ? 1_555 ? 9 AC1 22 SER A 211 ? SER A 211 . ? 3_555 ? 10 AC1 22 ARG A 213 ? ARG A 213 . ? 3_555 ? 11 AC1 22 ARG A 217 ? ARG A 217 . ? 1_555 ? 12 AC1 22 TYR A 248 ? TYR A 248 . ? 3_555 ? 13 AC1 22 VAL A 253 ? VAL A 253 . ? 1_555 ? 14 AC1 22 LYS A 254 ? LYS A 254 . ? 1_555 ? 15 AC1 22 LYS A 259 ? LYS A 259 . ? 1_555 ? 16 AC1 22 THR A 260 ? THR A 260 . ? 1_555 ? 17 AC1 22 LYS A 263 ? LYS A 263 . ? 1_555 ? 18 AC1 22 HOH D . ? HOH A 334 . ? 1_555 ? 19 AC1 22 HOH D . ? HOH A 338 . ? 3_555 ? 20 AC1 22 HOH D . ? HOH A 350 . ? 3_555 ? 21 AC1 22 HOH D . ? HOH A 352 . ? 3_555 ? 22 AC1 22 HOH D . ? HOH A 383 . ? 3_555 ? 23 AC2 13 PHE A 67 ? PHE A 67 . ? 3_555 ? 24 AC2 13 ARG A 104 ? ARG A 104 . ? 1_555 ? 25 AC2 13 ARG A 112 ? ARG A 112 . ? 3_555 ? 26 AC2 13 ASN A 129 ? ASN A 129 . ? 3_555 ? 27 AC2 13 MET A 139 ? MET A 139 . ? 1_555 ? 28 AC2 13 ASP A 141 ? ASP A 141 . ? 1_555 ? 29 AC2 13 SER A 148 ? SER A 148 . ? 3_555 ? 30 AC2 13 GLY A 166 ? GLY A 166 . ? 3_555 ? 31 AC2 13 VAL A 167 ? VAL A 167 . ? 3_555 ? 32 AC2 13 LEU A 168 ? LEU A 168 . ? 3_555 ? 33 AC2 13 GLU A 169 ? GLU A 169 . ? 3_555 ? 34 AC2 13 HOH D . ? HOH A 325 . ? 3_555 ? 35 AC2 13 HOH D . ? HOH A 383 . ? 3_555 ? # _database_PDB_matrix.entry_id 2TDT _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 2TDT _atom_sites.fract_transf_matrix[1][1] 0.010448 _atom_sites.fract_transf_matrix[1][2] 0.006032 _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] 0.012065 _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] 0.013738 _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 P 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 GLN 2 2 2 GLN GLN A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 ASN 6 6 6 ASN ASN A . n A 1 7 VAL 7 7 7 VAL VAL A . n A 1 8 ILE 8 8 8 ILE ILE A . n A 1 9 GLU 9 9 9 GLU GLU A . n A 1 10 SER 10 10 10 SER SER A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 PHE 12 12 12 PHE PHE A . n A 1 13 GLU 13 13 13 GLU GLU A . n A 1 14 ARG 14 14 14 ARG ARG A . n A 1 15 ARG 15 15 15 ARG ARG A . n A 1 16 ALA 16 16 16 ALA ALA A . n A 1 17 ASP 17 17 17 ASP ASP A . n A 1 18 ILE 18 18 18 ILE ILE A . n A 1 19 THR 19 19 19 THR THR A . n A 1 20 PRO 20 20 20 PRO PRO A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 ASN 22 22 22 ASN ASN A . n A 1 23 VAL 23 23 23 VAL VAL A . n A 1 24 ASP 24 24 24 ASP ASP A . n A 1 25 THR 25 25 25 THR THR A . n A 1 26 VAL 26 26 26 VAL VAL A . n A 1 27 THR 27 27 27 THR THR A . n A 1 28 ARG 28 28 28 ARG ARG A . n A 1 29 GLU 29 29 29 GLU GLU A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 ASN 32 32 32 ASN ASN A . n A 1 33 GLN 33 33 33 GLN GLN A . n A 1 34 VAL 34 34 34 VAL VAL A . n A 1 35 ILE 35 35 35 ILE ILE A . n A 1 36 GLY 36 36 36 GLY GLY A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 ASP 39 39 39 ASP ASP A . n A 1 40 SER 40 40 40 SER SER A . n A 1 41 GLY 41 41 41 GLY GLY A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ARG 44 44 44 ARG ARG A . n A 1 45 VAL 45 45 45 VAL VAL A . n A 1 46 ALA 46 46 46 ALA ALA A . n A 1 47 GLU 47 47 47 GLU GLU A . n A 1 48 LYS 48 48 48 LYS LYS A . n A 1 49 ILE 49 49 49 ILE ILE A . n A 1 50 ASP 50 50 50 ASP ASP A . n A 1 51 GLY 51 51 51 GLY GLY A . n A 1 52 GLN 52 52 52 GLN GLN A . n A 1 53 TRP 53 53 53 TRP TRP A . n A 1 54 VAL 54 54 54 VAL VAL A . n A 1 55 THR 55 55 55 THR THR A . n A 1 56 HIS 56 56 56 HIS HIS A . n A 1 57 GLN 57 57 57 GLN GLN A . n A 1 58 TRP 58 58 58 TRP TRP A . n A 1 59 LEU 59 59 59 LEU LEU A . n A 1 60 LYS 60 60 60 LYS LYS A . n A 1 61 LYS 61 61 61 LYS LYS A . n A 1 62 ALA 62 62 62 ALA ALA A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 LEU 64 64 64 LEU LEU A . n A 1 65 LEU 65 65 65 LEU LEU A . n A 1 66 SER 66 66 66 SER SER A . n A 1 67 PHE 67 67 67 PHE PHE A . n A 1 68 ARG 68 68 68 ARG ARG A . n A 1 69 ILE 69 69 69 ILE ILE A . n A 1 70 ASN 70 70 70 ASN ASN A . n A 1 71 ASP 71 71 71 ASP ASP A . n A 1 72 ASN 72 72 72 ASN ASN A . n A 1 73 LYS 73 73 73 LYS LYS A . n A 1 74 VAL 74 74 74 VAL VAL A . n A 1 75 MET 75 75 75 MET MET A . n A 1 76 ASP 76 76 76 ASP ASP A . n A 1 77 GLY 77 77 77 GLY GLY A . n A 1 78 ALA 78 78 78 ALA ALA A . n A 1 79 GLU 79 79 79 GLU GLU A . n A 1 80 THR 80 80 80 THR THR A . n A 1 81 ARG 81 81 81 ARG ARG A . n A 1 82 TYR 82 82 82 TYR TYR A . n A 1 83 TYR 83 83 83 TYR TYR A . n A 1 84 ASP 84 84 84 ASP ASP A . n A 1 85 LYS 85 85 85 LYS LYS A . n A 1 86 VAL 86 86 86 VAL VAL A . n A 1 87 PRO 87 87 87 PRO PRO A . n A 1 88 MET 88 88 88 MET MET A . n A 1 89 LYS 89 89 89 LYS LYS A . n A 1 90 PHE 90 90 90 PHE PHE A . n A 1 91 ALA 91 91 91 ALA ALA A . n A 1 92 ASP 92 92 92 ASP ASP A . n A 1 93 TYR 93 93 93 TYR TYR A . n A 1 94 ASP 94 94 94 ASP ASP A . n A 1 95 GLU 95 95 95 GLU GLU A . n A 1 96 ALA 96 96 96 ALA ALA A . n A 1 97 ARG 97 97 97 ARG ARG A . n A 1 98 PHE 98 98 98 PHE PHE A . n A 1 99 GLN 99 99 99 GLN GLN A . n A 1 100 LYS 100 100 100 LYS LYS A . n A 1 101 GLU 101 101 101 GLU GLU A . n A 1 102 GLY 102 102 102 GLY GLY A . n A 1 103 PHE 103 103 103 PHE PHE A . n A 1 104 ARG 104 104 104 ARG ARG A . n A 1 105 VAL 105 105 105 VAL VAL A . n A 1 106 VAL 106 106 106 VAL VAL A . n A 1 107 PRO 107 107 107 PRO PRO A . n A 1 108 PRO 108 108 108 PRO PRO A . n A 1 109 ALA 109 109 109 ALA ALA A . n A 1 110 THR 110 110 110 THR THR A . n A 1 111 VAL 111 111 111 VAL VAL A . n A 1 112 ARG 112 112 112 ARG ARG A . n A 1 113 GLN 113 113 113 GLN GLN A . n A 1 114 GLY 114 114 114 GLY GLY A . n A 1 115 ALA 115 115 115 ALA ALA A . n A 1 116 PHE 116 116 116 PHE PHE A . n A 1 117 ILE 117 117 117 ILE ILE A . n A 1 118 ALA 118 118 118 ALA ALA A . n A 1 119 ARG 119 119 119 ARG ARG A . n A 1 120 ASN 120 120 120 ASN ASN A . n A 1 121 THR 121 121 121 THR THR A . n A 1 122 VAL 122 122 122 VAL VAL A . n A 1 123 LEU 123 123 123 LEU LEU A . n A 1 124 MET 124 124 124 MET MET A . n A 1 125 PRO 125 125 125 PRO PRO A . n A 1 126 SER 126 126 126 SER SER A . n A 1 127 TYR 127 127 127 TYR TYR A . n A 1 128 VAL 128 128 128 VAL VAL A . n A 1 129 ASN 129 129 129 ASN ASN A . n A 1 130 ILE 130 130 130 ILE ILE A . n A 1 131 GLY 131 131 131 GLY GLY A . n A 1 132 ALA 132 132 132 ALA ALA A . n A 1 133 TYR 133 133 133 TYR TYR A . n A 1 134 VAL 134 134 134 VAL VAL A . n A 1 135 ASP 135 135 135 ASP ASP A . n A 1 136 GLU 136 136 136 GLU GLU A . n A 1 137 GLY 137 137 137 GLY GLY A . n A 1 138 THR 138 138 138 THR THR A . n A 1 139 MET 139 139 139 MET MET A . n A 1 140 VAL 140 140 140 VAL VAL A . n A 1 141 ASP 141 141 141 ASP ASP A . n A 1 142 THR 142 142 142 THR THR A . n A 1 143 TRP 143 143 143 TRP TRP A . n A 1 144 ALA 144 144 144 ALA ALA A . n A 1 145 THR 145 145 145 THR THR A . n A 1 146 VAL 146 146 146 VAL VAL A . n A 1 147 GLY 147 147 147 GLY GLY A . n A 1 148 SER 148 148 148 SER SER A . n A 1 149 CYS 149 149 149 CYS CYS A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 GLN 151 151 151 GLN GLN A . n A 1 152 ILE 152 152 152 ILE ILE A . n A 1 153 GLY 153 153 153 GLY GLY A . n A 1 154 LYS 154 154 154 LYS LYS A . n A 1 155 ASN 155 155 155 ASN ASN A . n A 1 156 VAL 156 156 156 VAL VAL A . n A 1 157 HIS 157 157 157 HIS HIS A . n A 1 158 LEU 158 158 158 LEU LEU A . n A 1 159 SER 159 159 159 SER SER A . n A 1 160 GLY 160 160 160 GLY GLY A . n A 1 161 GLY 161 161 161 GLY GLY A . n A 1 162 VAL 162 162 162 VAL VAL A . n A 1 163 GLY 163 163 163 GLY GLY A . n A 1 164 ILE 164 164 164 ILE ILE A . n A 1 165 GLY 165 165 165 GLY GLY A . n A 1 166 GLY 166 166 166 GLY GLY A . n A 1 167 VAL 167 167 167 VAL VAL A . n A 1 168 LEU 168 168 168 LEU LEU A . n A 1 169 GLU 169 169 169 GLU GLU A . n A 1 170 PRO 170 170 170 PRO PRO A . n A 1 171 LEU 171 171 171 LEU LEU A . n A 1 172 GLN 172 172 172 GLN GLN A . n A 1 173 ALA 173 173 173 ALA ALA A . n A 1 174 ASN 174 174 174 ASN ASN A . n A 1 175 PRO 175 175 175 PRO PRO A . n A 1 176 THR 176 176 176 THR THR A . n A 1 177 ILE 177 177 177 ILE ILE A . n A 1 178 ILE 178 178 178 ILE ILE A . n A 1 179 GLU 179 179 179 GLU GLU A . n A 1 180 ASP 180 180 180 ASP ASP A . n A 1 181 ASN 181 181 181 ASN ASN A . n A 1 182 CYS 182 182 182 CYS CYS A . n A 1 183 PHE 183 183 183 PHE PHE A . n A 1 184 ILE 184 184 184 ILE ILE A . n A 1 185 GLY 185 185 185 GLY GLY A . n A 1 186 ALA 186 186 186 ALA ALA A . n A 1 187 ARG 187 187 187 ARG ARG A . n A 1 188 SER 188 188 188 SER SER A . n A 1 189 GLU 189 189 189 GLU GLU A . n A 1 190 VAL 190 190 190 VAL VAL A . n A 1 191 VAL 191 191 191 VAL VAL A . n A 1 192 GLU 192 192 192 GLU GLU A . n A 1 193 GLY 193 193 193 GLY GLY A . n A 1 194 VAL 194 194 194 VAL VAL A . n A 1 195 ILE 195 195 195 ILE ILE A . n A 1 196 VAL 196 196 196 VAL VAL A . n A 1 197 GLU 197 197 197 GLU GLU A . n A 1 198 GLU 198 198 198 GLU GLU A . n A 1 199 GLY 199 199 199 GLY GLY A . n A 1 200 SER 200 200 200 SER SER A . n A 1 201 VAL 201 201 201 VAL VAL A . n A 1 202 ILE 202 202 202 ILE ILE A . n A 1 203 SER 203 203 203 SER SER A . n A 1 204 MET 204 204 204 MET MET A . n A 1 205 GLY 205 205 205 GLY GLY A . n A 1 206 VAL 206 206 206 VAL VAL A . n A 1 207 TYR 207 207 207 TYR TYR A . n A 1 208 LEU 208 208 208 LEU LEU A . n A 1 209 GLY 209 209 209 GLY GLY A . n A 1 210 GLN 210 210 210 GLN GLN A . n A 1 211 SER 211 211 211 SER SER A . n A 1 212 THR 212 212 212 THR THR A . n A 1 213 ARG 213 213 213 ARG ARG A . n A 1 214 ILE 214 214 214 ILE ILE A . n A 1 215 TYR 215 215 215 TYR TYR A . n A 1 216 ASP 216 216 216 ASP ASP A . n A 1 217 ARG 217 217 217 ARG ARG A . n A 1 218 GLU 218 218 218 GLU GLU A . n A 1 219 THR 219 219 219 THR THR A . n A 1 220 GLY 220 220 220 GLY GLY A . n A 1 221 GLU 221 221 221 GLU GLU A . n A 1 222 ILE 222 222 222 ILE ILE A . n A 1 223 HIS 223 223 223 HIS HIS A . n A 1 224 TYR 224 224 224 TYR TYR A . n A 1 225 GLY 225 225 225 GLY GLY A . n A 1 226 ARG 226 226 226 ARG ARG A . n A 1 227 VAL 227 227 227 VAL VAL A . n A 1 228 PRO 228 228 228 PRO PRO A . n A 1 229 ALA 229 229 229 ALA ALA A . n A 1 230 GLY 230 230 230 GLY GLY A . n A 1 231 SER 231 231 231 SER SER A . n A 1 232 VAL 232 232 232 VAL VAL A . n A 1 233 VAL 233 233 233 VAL VAL A . n A 1 234 VAL 234 234 234 VAL VAL A . n A 1 235 SER 235 235 235 SER SER A . n A 1 236 GLY 236 236 236 GLY GLY A . n A 1 237 ASN 237 237 237 ASN ASN A . n A 1 238 LEU 238 238 238 LEU LEU A . n A 1 239 PRO 239 239 239 PRO PRO A . n A 1 240 SER 240 240 240 SER SER A . n A 1 241 LYS 241 241 241 LYS LYS A . n A 1 242 ASP 242 242 242 ASP ASP A . n A 1 243 GLY 243 243 243 GLY GLY A . n A 1 244 SER 244 244 244 SER SER A . n A 1 245 TYR 245 245 245 TYR TYR A . n A 1 246 SER 246 246 246 SER SER A . n A 1 247 LEU 247 247 247 LEU LEU A . n A 1 248 TYR 248 248 248 TYR TYR A . n A 1 249 CYS 249 249 249 CYS CYS A . n A 1 250 ALA 250 250 250 ALA ALA A . n A 1 251 VAL 251 251 251 VAL VAL A . n A 1 252 ILE 252 252 252 ILE ILE A . n A 1 253 VAL 253 253 253 VAL VAL A . n A 1 254 LYS 254 254 254 LYS LYS A . n A 1 255 LYS 255 255 255 LYS LYS A . n A 1 256 VAL 256 256 256 VAL VAL A . n A 1 257 ASP 257 257 257 ASP ASP A . n A 1 258 ALA 258 258 258 ALA ALA A . n A 1 259 LYS 259 259 259 LYS LYS A . n A 1 260 THR 260 260 260 THR THR A . n A 1 261 ARG 261 261 261 ARG ARG A . n A 1 262 GLY 262 262 262 GLY GLY A . n A 1 263 LYS 263 263 263 LYS LYS A . n A 1 264 VAL 264 264 264 VAL VAL A . n A 1 265 GLY 265 265 265 GLY GLY A . n A 1 266 ILE 266 266 266 ILE ILE A . n A 1 267 ASN 267 267 267 ASN ASN A . n A 1 268 GLU 268 268 268 GLU GLU A . n A 1 269 LEU 269 269 269 LEU LEU A . n A 1 270 LEU 270 270 270 LEU LEU A . n A 1 271 ARG 271 271 271 ARG ARG A . n A 1 272 THR 272 272 272 THR THR A . n A 1 273 ILE 273 273 273 ILE ILE A . n A 1 274 ASP 274 274 274 ASP ASP 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 COA 1 280 280 COA COA A . C 3 NPI 1 281 281 NPI NPI A . D 4 HOH 1 301 301 HOH HOH A . D 4 HOH 2 302 302 HOH HOH A . D 4 HOH 3 303 303 HOH HOH A . D 4 HOH 4 304 304 HOH HOH A . D 4 HOH 5 305 305 HOH HOH A . D 4 HOH 6 306 306 HOH HOH A . D 4 HOH 7 307 307 HOH HOH A . D 4 HOH 8 308 308 HOH HOH A . D 4 HOH 9 309 309 HOH HOH A . D 4 HOH 10 310 310 HOH HOH A . D 4 HOH 11 311 311 HOH HOH A . D 4 HOH 12 312 312 HOH HOH A . D 4 HOH 13 313 313 HOH HOH A . D 4 HOH 14 314 314 HOH HOH A . D 4 HOH 15 315 315 HOH HOH A . D 4 HOH 16 316 316 HOH HOH A . D 4 HOH 17 317 317 HOH HOH A . D 4 HOH 18 318 318 HOH HOH A . D 4 HOH 19 319 319 HOH HOH A . D 4 HOH 20 320 320 HOH HOH A . D 4 HOH 21 321 321 HOH HOH A . D 4 HOH 22 322 322 HOH HOH A . D 4 HOH 23 323 323 HOH HOH A . D 4 HOH 24 324 324 HOH HOH A . D 4 HOH 25 325 325 HOH HOH A . D 4 HOH 26 326 326 HOH HOH A . D 4 HOH 27 327 327 HOH HOH A . D 4 HOH 28 328 328 HOH HOH A . D 4 HOH 29 329 329 HOH HOH A . D 4 HOH 30 330 330 HOH HOH A . D 4 HOH 31 331 331 HOH HOH A . D 4 HOH 32 332 332 HOH HOH A . D 4 HOH 33 333 333 HOH HOH A . D 4 HOH 34 334 334 HOH HOH A . D 4 HOH 35 335 335 HOH HOH A . D 4 HOH 36 336 336 HOH HOH A . D 4 HOH 37 337 337 HOH HOH A . D 4 HOH 38 338 338 HOH HOH A . D 4 HOH 39 339 339 HOH HOH A . D 4 HOH 40 340 340 HOH HOH A . D 4 HOH 41 341 341 HOH HOH A . D 4 HOH 42 342 342 HOH HOH A . D 4 HOH 43 343 343 HOH HOH A . D 4 HOH 44 344 344 HOH HOH A . D 4 HOH 45 345 345 HOH HOH A . D 4 HOH 46 346 346 HOH HOH A . D 4 HOH 47 347 347 HOH HOH A . D 4 HOH 48 348 348 HOH HOH A . D 4 HOH 49 349 349 HOH HOH A . D 4 HOH 50 350 350 HOH HOH A . D 4 HOH 51 351 351 HOH HOH A . D 4 HOH 52 352 352 HOH HOH A . D 4 HOH 53 353 353 HOH HOH A . D 4 HOH 54 354 354 HOH HOH A . D 4 HOH 55 355 355 HOH HOH A . D 4 HOH 56 356 356 HOH HOH A . D 4 HOH 57 357 357 HOH HOH A . D 4 HOH 58 358 358 HOH HOH A . D 4 HOH 59 359 359 HOH HOH A . D 4 HOH 60 360 360 HOH HOH A . D 4 HOH 61 361 361 HOH HOH A . D 4 HOH 62 362 362 HOH HOH A . D 4 HOH 63 363 363 HOH HOH A . D 4 HOH 64 364 364 HOH HOH A . D 4 HOH 65 365 365 HOH HOH A . D 4 HOH 66 366 366 HOH HOH A . D 4 HOH 67 367 367 HOH HOH A . D 4 HOH 68 368 368 HOH HOH A . D 4 HOH 69 369 369 HOH HOH A . D 4 HOH 70 370 370 HOH HOH A . D 4 HOH 71 371 371 HOH HOH A . D 4 HOH 72 372 372 HOH HOH A . D 4 HOH 73 373 373 HOH HOH A . D 4 HOH 74 374 374 HOH HOH A . D 4 HOH 75 375 375 HOH HOH A . D 4 HOH 76 376 376 HOH HOH A . D 4 HOH 77 377 377 HOH HOH A . D 4 HOH 78 378 378 HOH HOH A . D 4 HOH 79 379 379 HOH HOH A . D 4 HOH 80 380 380 HOH HOH A . D 4 HOH 81 381 381 HOH HOH A . D 4 HOH 82 382 382 HOH HOH A . D 4 HOH 83 383 383 HOH HOH A . D 4 HOH 84 384 384 HOH HOH A . D 4 HOH 85 385 385 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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)' 18440 ? 1 MORE -39 ? 1 'SSA (A^2)' 26680 ? # 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' 2_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 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 1998-10-14 2 'Structure model' 1 1 2008-03-25 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-08-17 5 'Structure model' 1 4 2023-08-09 # _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_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Non-polymer description' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' Other 8 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' database_2 2 5 'Structure model' pdbx_database_status 3 5 'Structure model' pdbx_initial_refinement_model 4 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_database_status.process_site' 4 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 TNT refinement 5E ? 2 X-PLOR refinement . ? 3 XDS 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 X-PLOR phasing . ? 6 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 GLY _pdbx_validate_rmsd_angle.auth_seq_id_1 77 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CA _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 GLY _pdbx_validate_rmsd_angle.auth_seq_id_2 77 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 C _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 GLY _pdbx_validate_rmsd_angle.auth_seq_id_3 77 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 96.96 _pdbx_validate_rmsd_angle.angle_target_value 113.10 _pdbx_validate_rmsd_angle.angle_deviation -16.14 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.50 _pdbx_validate_rmsd_angle.linker_flag 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 PRO A 108 ? ? -104.75 48.07 2 1 SER A 126 ? ? -173.37 -175.99 3 1 SER A 159 ? ? -65.83 -180.00 # 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 GLN 2 ? CG ? A GLN 2 CG 2 1 Y 1 A GLN 2 ? CD ? A GLN 2 CD 3 1 Y 1 A GLN 2 ? OE1 ? A GLN 2 OE1 4 1 Y 1 A GLN 2 ? NE2 ? A GLN 2 NE2 5 1 Y 1 A GLU 13 ? CG ? A GLU 13 CG 6 1 Y 1 A GLU 13 ? CD ? A GLU 13 CD 7 1 Y 1 A GLU 13 ? OE1 ? A GLU 13 OE1 8 1 Y 1 A GLU 13 ? OE2 ? A GLU 13 OE2 9 1 Y 1 A GLN 52 ? CG ? A GLN 52 CG 10 1 Y 1 A GLN 52 ? CD ? A GLN 52 CD 11 1 Y 1 A GLN 52 ? OE1 ? A GLN 52 OE1 12 1 Y 1 A GLN 52 ? NE2 ? A GLN 52 NE2 13 1 Y 1 A ASP 92 ? CG ? A ASP 92 CG 14 1 Y 1 A ASP 92 ? OD1 ? A ASP 92 OD1 15 1 Y 1 A ASP 92 ? OD2 ? A ASP 92 OD2 16 1 Y 1 A LYS 241 ? CG ? A LYS 241 CG 17 1 Y 1 A LYS 241 ? CD ? A LYS 241 CD 18 1 Y 1 A LYS 241 ? CE ? A LYS 241 CE 19 1 Y 1 A LYS 241 ? NZ ? A LYS 241 NZ 20 1 Y 1 A ILE 273 ? CG1 ? A ILE 273 CG1 21 1 Y 1 A ILE 273 ? CG2 ? A ILE 273 CG2 22 1 Y 1 A ILE 273 ? CD1 ? A ILE 273 CD1 23 1 Y 1 A ASP 274 ? CG ? A ASP 274 CG 24 1 Y 1 A ASP 274 ? OD1 ? A ASP 274 OD1 25 1 Y 1 A ASP 274 ? OD2 ? A ASP 274 OD2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COENZYME A' COA 3 '(2S)-2-aminoheptanedioic acid' NPI 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1TDT _pdbx_initial_refinement_model.details 'PDB ENTRY 1TDT' #