data_4LYE # _entry.id 4LYE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4LYE RCSB RCSB081241 WWPDB D_1000081241 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4LXG 'DxnB2 wild type' unspecified PDB 4LYD 'DxnB2 S105A' unspecified PDB 4LXH 'DxnB2 S105A in complex with 3-Cl-HOPDA' unspecified PDB 4LXI 'DxnB2 S105A in complex with 5,8-diF-HOPDA' unspecified # _pdbx_database_status.entry_id 4LYE _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-07-31 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ghosh, S.' 1 'Bolin, J.T.' 2 # _citation.id primary _citation.title 'A substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase.' _citation.journal_abbrev Biochemistry _citation.journal_volume 52 _citation.page_first 7428 _citation.page_last 7438 _citation.year 2013 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24067021 _citation.pdbx_database_id_DOI 10.1021/bi401156a # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ruzzini, A.C.' 1 primary 'Bhowmik, S.' 2 primary 'Ghosh, S.' 3 primary 'Yam, K.C.' 4 primary 'Bolin, J.T.' 5 primary 'Eltis, L.D.' 6 # _cell.length_a 65.715 _cell.length_b 65.715 _cell.length_c 339.252 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 4LYE _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.entry_id 4LYE _symmetry.Int_Tables_number 179 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'MCP Hydrolase' 30208.531 1 3.7.1.8 S105A ? ? 2 non-polymer syn '(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE' 217.197 1 ? ? ? ? 3 water nat water 18.015 72 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Alpha/beta hydrolase fold' # _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 ;MFEQFESKFIDCDGIRTHYIEMGEGDPLVLVHGGGAGADGRSNFADNFPIFARHMRVIAYDMVGFGQTDAPDPAGFAYTQ AARTDHLISFIKALGLSKICLIGNAMGGTTACGAALKAPELIDRLVLMGAAVNISPDDMVANRDDLAAVMSYDGSEEGMR KIIAALTHSYQPTDDIVHYRHEASLRPTTTAAYKATMGWAKQNGLYYSPEQLASLTMPVLVLGGKNDVMVPVRKVIDQIL AIPQAIGHVFPNCGHWVMIEYPEEFCTQTLHFFGKLD ; _entity_poly.pdbx_seq_one_letter_code_can ;MFEQFESKFIDCDGIRTHYIEMGEGDPLVLVHGGGAGADGRSNFADNFPIFARHMRVIAYDMVGFGQTDAPDPAGFAYTQ AARTDHLISFIKALGLSKICLIGNAMGGTTACGAALKAPELIDRLVLMGAAVNISPDDMVANRDDLAAVMSYDGSEEGMR KIIAALTHSYQPTDDIVHYRHEASLRPTTTAAYKATMGWAKQNGLYYSPEQLASLTMPVLVLGGKNDVMVPVRKVIDQIL AIPQAIGHVFPNCGHWVMIEYPEEFCTQTLHFFGKLD ; _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 PHE n 1 3 GLU n 1 4 GLN n 1 5 PHE n 1 6 GLU n 1 7 SER n 1 8 LYS n 1 9 PHE n 1 10 ILE n 1 11 ASP n 1 12 CYS n 1 13 ASP n 1 14 GLY n 1 15 ILE n 1 16 ARG n 1 17 THR n 1 18 HIS n 1 19 TYR n 1 20 ILE n 1 21 GLU n 1 22 MET n 1 23 GLY n 1 24 GLU n 1 25 GLY n 1 26 ASP n 1 27 PRO n 1 28 LEU n 1 29 VAL n 1 30 LEU n 1 31 VAL n 1 32 HIS n 1 33 GLY n 1 34 GLY n 1 35 GLY n 1 36 ALA n 1 37 GLY n 1 38 ALA n 1 39 ASP n 1 40 GLY n 1 41 ARG n 1 42 SER n 1 43 ASN n 1 44 PHE n 1 45 ALA n 1 46 ASP n 1 47 ASN n 1 48 PHE n 1 49 PRO n 1 50 ILE n 1 51 PHE n 1 52 ALA n 1 53 ARG n 1 54 HIS n 1 55 MET n 1 56 ARG n 1 57 VAL n 1 58 ILE n 1 59 ALA n 1 60 TYR n 1 61 ASP n 1 62 MET n 1 63 VAL n 1 64 GLY n 1 65 PHE n 1 66 GLY n 1 67 GLN n 1 68 THR n 1 69 ASP n 1 70 ALA n 1 71 PRO n 1 72 ASP n 1 73 PRO n 1 74 ALA n 1 75 GLY n 1 76 PHE n 1 77 ALA n 1 78 TYR n 1 79 THR n 1 80 GLN n 1 81 ALA n 1 82 ALA n 1 83 ARG n 1 84 THR n 1 85 ASP n 1 86 HIS n 1 87 LEU n 1 88 ILE n 1 89 SER n 1 90 PHE n 1 91 ILE n 1 92 LYS n 1 93 ALA n 1 94 LEU n 1 95 GLY n 1 96 LEU n 1 97 SER n 1 98 LYS n 1 99 ILE n 1 100 CYS n 1 101 LEU n 1 102 ILE n 1 103 GLY n 1 104 ASN n 1 105 ALA n 1 106 MET n 1 107 GLY n 1 108 GLY n 1 109 THR n 1 110 THR n 1 111 ALA n 1 112 CYS n 1 113 GLY n 1 114 ALA n 1 115 ALA n 1 116 LEU n 1 117 LYS n 1 118 ALA n 1 119 PRO n 1 120 GLU n 1 121 LEU n 1 122 ILE n 1 123 ASP n 1 124 ARG n 1 125 LEU n 1 126 VAL n 1 127 LEU n 1 128 MET n 1 129 GLY n 1 130 ALA n 1 131 ALA n 1 132 VAL n 1 133 ASN n 1 134 ILE n 1 135 SER n 1 136 PRO n 1 137 ASP n 1 138 ASP n 1 139 MET n 1 140 VAL n 1 141 ALA n 1 142 ASN n 1 143 ARG n 1 144 ASP n 1 145 ASP n 1 146 LEU n 1 147 ALA n 1 148 ALA n 1 149 VAL n 1 150 MET n 1 151 SER n 1 152 TYR n 1 153 ASP n 1 154 GLY n 1 155 SER n 1 156 GLU n 1 157 GLU n 1 158 GLY n 1 159 MET n 1 160 ARG n 1 161 LYS n 1 162 ILE n 1 163 ILE n 1 164 ALA n 1 165 ALA n 1 166 LEU n 1 167 THR n 1 168 HIS n 1 169 SER n 1 170 TYR n 1 171 GLN n 1 172 PRO n 1 173 THR n 1 174 ASP n 1 175 ASP n 1 176 ILE n 1 177 VAL n 1 178 HIS n 1 179 TYR n 1 180 ARG n 1 181 HIS n 1 182 GLU n 1 183 ALA n 1 184 SER n 1 185 LEU n 1 186 ARG n 1 187 PRO n 1 188 THR n 1 189 THR n 1 190 THR n 1 191 ALA n 1 192 ALA n 1 193 TYR n 1 194 LYS n 1 195 ALA n 1 196 THR n 1 197 MET n 1 198 GLY n 1 199 TRP n 1 200 ALA n 1 201 LYS n 1 202 GLN n 1 203 ASN n 1 204 GLY n 1 205 LEU n 1 206 TYR n 1 207 TYR n 1 208 SER n 1 209 PRO n 1 210 GLU n 1 211 GLN n 1 212 LEU n 1 213 ALA n 1 214 SER n 1 215 LEU n 1 216 THR n 1 217 MET n 1 218 PRO n 1 219 VAL n 1 220 LEU n 1 221 VAL n 1 222 LEU n 1 223 GLY n 1 224 GLY n 1 225 LYS n 1 226 ASN n 1 227 ASP n 1 228 VAL n 1 229 MET n 1 230 VAL n 1 231 PRO n 1 232 VAL n 1 233 ARG n 1 234 LYS n 1 235 VAL n 1 236 ILE n 1 237 ASP n 1 238 GLN n 1 239 ILE n 1 240 LEU n 1 241 ALA n 1 242 ILE n 1 243 PRO n 1 244 GLN n 1 245 ALA n 1 246 ILE n 1 247 GLY n 1 248 HIS n 1 249 VAL n 1 250 PHE n 1 251 PRO n 1 252 ASN n 1 253 CYS n 1 254 GLY n 1 255 HIS n 1 256 TRP n 1 257 VAL n 1 258 MET n 1 259 ILE n 1 260 GLU n 1 261 TYR n 1 262 PRO n 1 263 GLU n 1 264 GLU n 1 265 PHE n 1 266 CYS n 1 267 THR n 1 268 GLN n 1 269 THR n 1 270 LEU n 1 271 HIS n 1 272 PHE n 1 273 PHE n 1 274 GLY n 1 275 LYS n 1 276 LEU n 1 277 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 ? _entity_src_gen.pdbx_gene_src_gene 'dxnB2, Swit_3055' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain RW1 _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 'Sphingomonas wittichii' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 392499 _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 668369 _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 DH5a _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 pEMDXN1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A5VAT9_SPHWW _struct_ref.pdbx_db_accession A5VAT9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MFEQFESKFIDCDGIRTHYIEMGEGDPLVLVHGGGAGADGRSNFADNFPIFARHMRVIAYDMVGFGQTDAPDPAGFAYTQ AARTDHLISFIKALGLSKICLIGNSMGGTTACGAALKAPELIDRLVLMGAAVNISPDDMVANRDDLAAVMSYDGSEEGMR KIIAALTHSYQPTDDIVHYRHEASLRPTTTAAYKATMGWAKQNGLYYSPEQLASLTMPVLVLGGKNDVMVPVRKVIDQIL AIPQAIGHVFPNCGHWVMIEYPEEFCTQTLHFFGKLD ; _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 4LYE _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 277 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A5VAT9 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 277 _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 277 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4LYE _struct_ref_seq_dif.mon_id ALA _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 105 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code A5VAT9 _struct_ref_seq_dif.db_mon_id SER _struct_ref_seq_dif.pdbx_seq_db_seq_num 105 _struct_ref_seq_dif.details 'ENGINEERED MUTATION' _struct_ref_seq_dif.pdbx_auth_seq_num 105 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 HPK non-polymer . '(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE' ? 'C12 H9 O4 -1' 217.197 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 4LYE _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.50 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 64.86 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 6.8 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '1.8 M sodium malonate, pH 6.8, vapor diffusion, sitting drop, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-08-04 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Ge(111)' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9787 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-BM-C' _diffrn_source.pdbx_wavelength_list 0.9787 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-BM-C # _reflns.entry_id 4LYE _reflns.d_resolution_high 2.330 _reflns.d_resolution_low 50.000 _reflns.number_obs 19800 _reflns.pdbx_Rmerge_I_obs 0.090 _reflns.pdbx_netI_over_sigmaI 11.500 _reflns.pdbx_chi_squared 1.187 _reflns.pdbx_redundancy 10.700 _reflns.percent_possible_obs 99.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.330 2.410 ? ? ? 0.459 ? ? 0.999 10.200 ? 1893 98.500 1 1 2.410 2.510 ? ? ? 0.369 ? ? 1.068 11.000 ? 1914 99.900 2 1 2.510 2.620 ? ? ? 0.313 ? ? 1.177 11.100 ? 1933 99.900 3 1 2.620 2.760 ? ? ? 0.245 ? ? 1.271 11.000 ? 1940 100.000 4 1 2.760 2.940 ? ? ? 0.181 ? ? 1.449 11.100 ? 1919 100.000 5 1 2.940 3.160 ? ? ? 0.135 ? ? 1.432 10.900 ? 1966 99.900 6 1 3.160 3.480 ? ? ? 0.104 ? ? 1.258 10.900 ? 1975 100.000 7 1 3.480 3.980 ? ? ? 0.083 ? ? 1.130 10.800 ? 1988 100.000 8 1 3.980 5.020 ? ? ? 0.074 ? ? 1.075 10.400 ? 2064 100.000 9 1 5.020 50.000 ? ? ? 0.043 ? ? 0.973 9.300 ? 2208 97.200 10 1 # _refine.entry_id 4LYE _refine.ls_d_res_high 2.3300 _refine.ls_d_res_low 21.1400 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.6400 _refine.ls_number_reflns_obs 19693 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1872 _refine.ls_R_factor_R_work 0.1848 _refine.ls_wR_factor_R_work 0.1889 _refine.ls_R_factor_R_free 0.2339 _refine.ls_wR_factor_R_free 0.2383 _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_number_reflns_R_free 1006 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 48.3882 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.5800 _refine.aniso_B[2][2] 0.5800 _refine.aniso_B[3][3] -1.8800 _refine.aniso_B[1][2] 0.5800 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9640 _refine.correlation_coeff_Fo_to_Fc_free 0.9410 _refine.overall_SU_R_Cruickshank_DPI 0.2068 _refine.overall_SU_R_free 0.1904 _refine.pdbx_overall_ESU_R 0.2070 _refine.pdbx_overall_ESU_R_Free 0.1900 _refine.overall_SU_ML 0.1430 _refine.overall_SU_B 6.3320 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8241 _refine.B_iso_max 112.240 _refine.B_iso_min 17.210 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2108 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 16 _refine_hist.number_atoms_solvent 72 _refine_hist.number_atoms_total 2196 _refine_hist.d_res_high 2.3300 _refine_hist.d_res_low 21.1400 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 2174 0.011 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 2044 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2947 1.415 1.959 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 4699 0.764 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 275 5.895 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 94 34.462 23.936 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 344 15.924 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 11 16.502 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 322 0.078 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 2494 0.006 0.021 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 504 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 1103 2.916 4.598 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 1102 2.915 4.594 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 1377 4.312 6.890 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.3300 _refine_ls_shell.d_res_low 2.3900 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.7900 _refine_ls_shell.number_reflns_R_work 1331 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2900 _refine_ls_shell.R_factor_R_free 0.3710 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 73 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1404 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4LYE _struct.title 'Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with substrate HOPDA' _struct.pdbx_descriptor 'MCP Hydrolase (E.C.3.7.1.8)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4LYE _struct_keywords.text ;meta-cleavage product hydrolase, C-C bond hydrolase, alpha-beta hydrolase, dibenzo-p-dioxin degradation, dibenzofuran degradation, HYDROLASE ; _struct_keywords.pdbx_keywords HYDROLASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 39 ? ALA A 45 ? ASP A 39 ALA A 45 1 ? 7 HELX_P HELX_P2 2 ASN A 47 ? ARG A 53 ? ASN A 47 ARG A 53 1 ? 7 HELX_P HELX_P3 3 THR A 79 ? LEU A 94 ? THR A 79 LEU A 94 1 ? 16 HELX_P HELX_P4 4 ALA A 105 ? ALA A 118 ? ALA A 105 ALA A 118 1 ? 14 HELX_P HELX_P5 5 SER A 135 ? ASN A 142 ? SER A 135 ASN A 142 1 ? 8 HELX_P HELX_P6 6 ASN A 142 ? SER A 151 ? ASN A 142 SER A 151 1 ? 10 HELX_P HELX_P7 7 SER A 155 ? THR A 167 ? SER A 155 THR A 167 1 ? 13 HELX_P HELX_P8 8 THR A 173 ? LEU A 185 ? THR A 173 LEU A 185 1 ? 13 HELX_P HELX_P9 9 ARG A 186 ? GLY A 204 ? ARG A 186 GLY A 204 1 ? 19 HELX_P HELX_P10 10 SER A 208 ? SER A 214 ? SER A 208 SER A 214 1 ? 7 HELX_P HELX_P11 11 PRO A 231 ? ILE A 242 ? PRO A 231 ILE A 242 1 ? 12 HELX_P HELX_P12 12 TRP A 256 ? TYR A 261 ? TRP A 256 TYR A 261 1 ? 6 HELX_P HELX_P13 13 TYR A 261 ? PHE A 273 ? TYR A 261 PHE A 273 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 8 ? B ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? parallel A 6 7 ? parallel A 7 8 ? parallel B 1 2 ? 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 LYS A 8 ? CYS A 12 ? LYS A 8 CYS A 12 A 2 ILE A 15 ? MET A 22 ? ILE A 15 MET A 22 A 3 ARG A 56 ? TYR A 60 ? ARG A 56 TYR A 60 A 4 PRO A 27 ? VAL A 31 ? PRO A 27 VAL A 31 A 5 ILE A 99 ? ASN A 104 ? ILE A 99 ASN A 104 A 6 ILE A 122 ? MET A 128 ? ILE A 122 MET A 128 A 7 VAL A 219 ? GLY A 224 ? VAL A 219 GLY A 224 A 8 ILE A 246 ? PHE A 250 ? ILE A 246 PHE A 250 B 1 ASN A 133 ? ILE A 134 ? ASN A 133 ILE A 134 B 2 LEU A 205 ? TYR A 206 ? LEU A 205 TYR A 206 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N CYS A 12 ? N CYS A 12 O ILE A 15 ? O ILE A 15 A 2 3 N MET A 22 ? N MET A 22 O VAL A 57 ? O VAL A 57 A 3 4 O ILE A 58 ? O ILE A 58 N LEU A 30 ? N LEU A 30 A 4 5 N VAL A 31 ? N VAL A 31 O ILE A 102 ? O ILE A 102 A 5 6 N GLY A 103 ? N GLY A 103 O MET A 128 ? O MET A 128 A 6 7 N LEU A 127 ? N LEU A 127 O LEU A 222 ? O LEU A 222 A 7 8 N VAL A 219 ? N VAL A 219 O ILE A 246 ? O ILE A 246 B 1 2 N ILE A 134 ? N ILE A 134 O LEU A 205 ? O LEU A 205 # _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 16 _struct_site.details 'BINDING SITE FOR RESIDUE HPK 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 16 GLY A 33 ? GLY A 33 . ? 1_555 ? 2 AC1 16 GLY A 34 ? GLY A 34 . ? 1_555 ? 3 AC1 16 GLY A 35 ? GLY A 35 . ? 1_555 ? 4 AC1 16 ALA A 38 ? ALA A 38 . ? 1_555 ? 5 AC1 16 ASN A 43 ? ASN A 43 . ? 1_555 ? 6 AC1 16 ASN A 104 ? ASN A 104 . ? 1_555 ? 7 AC1 16 ALA A 105 ? ALA A 105 . ? 1_555 ? 8 AC1 16 MET A 106 ? MET A 106 . ? 1_555 ? 9 AC1 16 LEU A 146 ? LEU A 146 . ? 1_555 ? 10 AC1 16 MET A 150 ? MET A 150 . ? 1_555 ? 11 AC1 16 LEU A 166 ? LEU A 166 . ? 1_555 ? 12 AC1 16 ARG A 180 ? ARG A 180 . ? 1_555 ? 13 AC1 16 MET A 229 ? MET A 229 . ? 1_555 ? 14 AC1 16 HIS A 255 ? HIS A 255 . ? 1_555 ? 15 AC1 16 TRP A 256 ? TRP A 256 . ? 1_555 ? 16 AC1 16 HOH C . ? HOH A 469 . ? 1_555 ? # _atom_sites.entry_id 4LYE _atom_sites.fract_transf_matrix[1][1] 0.015217 _atom_sites.fract_transf_matrix[1][2] 0.008786 _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] 0.017571 _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] 0.002948 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 PHE 2 2 2 PHE PHE A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 PHE 5 5 5 PHE PHE A . n A 1 6 GLU 6 6 6 GLU GLU A . n A 1 7 SER 7 7 7 SER SER A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 ILE 10 10 10 ILE ILE A . n A 1 11 ASP 11 11 11 ASP ASP A . n A 1 12 CYS 12 12 12 CYS CYS A . n A 1 13 ASP 13 13 13 ASP ASP A . n A 1 14 GLY 14 14 14 GLY GLY A . n A 1 15 ILE 15 15 15 ILE ILE A . n A 1 16 ARG 16 16 16 ARG ARG A . n A 1 17 THR 17 17 17 THR THR A . n A 1 18 HIS 18 18 18 HIS HIS A . n A 1 19 TYR 19 19 19 TYR TYR A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 GLU 21 21 21 GLU GLU A . n A 1 22 MET 22 22 22 MET MET A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 GLU 24 24 24 GLU GLU A . n A 1 25 GLY 25 25 25 GLY GLY A . n A 1 26 ASP 26 26 26 ASP ASP A . n A 1 27 PRO 27 27 27 PRO PRO A . n A 1 28 LEU 28 28 28 LEU LEU A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 LEU 30 30 30 LEU LEU A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 HIS 32 32 32 HIS HIS A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 ALA 36 36 36 ALA ALA A . n A 1 37 GLY 37 37 37 GLY GLY A . n A 1 38 ALA 38 38 38 ALA ALA A . n A 1 39 ASP 39 39 39 ASP ASP A . n A 1 40 GLY 40 40 40 GLY GLY A . n A 1 41 ARG 41 41 41 ARG ARG A . n A 1 42 SER 42 42 42 SER SER A . n A 1 43 ASN 43 43 43 ASN ASN A . n A 1 44 PHE 44 44 44 PHE PHE A . n A 1 45 ALA 45 45 45 ALA ALA A . n A 1 46 ASP 46 46 46 ASP ASP A . n A 1 47 ASN 47 47 47 ASN ASN A . n A 1 48 PHE 48 48 48 PHE PHE A . n A 1 49 PRO 49 49 49 PRO PRO A . n A 1 50 ILE 50 50 50 ILE ILE A . n A 1 51 PHE 51 51 51 PHE PHE A . n A 1 52 ALA 52 52 52 ALA ALA A . n A 1 53 ARG 53 53 53 ARG ARG A . n A 1 54 HIS 54 54 54 HIS HIS A . n A 1 55 MET 55 55 55 MET MET A . n A 1 56 ARG 56 56 56 ARG ARG A . n A 1 57 VAL 57 57 57 VAL VAL A . n A 1 58 ILE 58 58 58 ILE ILE A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 TYR 60 60 60 TYR TYR A . n A 1 61 ASP 61 61 61 ASP ASP A . n A 1 62 MET 62 62 62 MET MET A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 GLY 64 64 64 GLY GLY A . n A 1 65 PHE 65 65 65 PHE PHE A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 GLN 67 67 67 GLN GLN A . n A 1 68 THR 68 68 68 THR THR A . n A 1 69 ASP 69 69 69 ASP ASP A . n A 1 70 ALA 70 70 70 ALA ALA A . n A 1 71 PRO 71 71 71 PRO PRO A . n A 1 72 ASP 72 72 72 ASP ASP A . n A 1 73 PRO 73 73 73 PRO PRO A . n A 1 74 ALA 74 74 74 ALA ALA A . n A 1 75 GLY 75 75 75 GLY GLY A . n A 1 76 PHE 76 76 76 PHE PHE A . n A 1 77 ALA 77 77 77 ALA ALA A . n A 1 78 TYR 78 78 78 TYR TYR A . n A 1 79 THR 79 79 79 THR THR A . n A 1 80 GLN 80 80 80 GLN GLN A . n A 1 81 ALA 81 81 81 ALA ALA A . n A 1 82 ALA 82 82 82 ALA ALA A . n A 1 83 ARG 83 83 83 ARG ARG A . n A 1 84 THR 84 84 84 THR THR A . n A 1 85 ASP 85 85 85 ASP ASP A . n A 1 86 HIS 86 86 86 HIS HIS A . n A 1 87 LEU 87 87 87 LEU LEU A . n A 1 88 ILE 88 88 88 ILE ILE A . n A 1 89 SER 89 89 89 SER SER A . n A 1 90 PHE 90 90 90 PHE PHE A . n A 1 91 ILE 91 91 91 ILE ILE A . n A 1 92 LYS 92 92 92 LYS LYS A . n A 1 93 ALA 93 93 93 ALA ALA A . n A 1 94 LEU 94 94 94 LEU LEU A . n A 1 95 GLY 95 95 95 GLY GLY A . n A 1 96 LEU 96 96 96 LEU LEU A . n A 1 97 SER 97 97 97 SER SER A . n A 1 98 LYS 98 98 98 LYS LYS A . n A 1 99 ILE 99 99 99 ILE ILE A . n A 1 100 CYS 100 100 100 CYS CYS A . n A 1 101 LEU 101 101 101 LEU LEU A . n A 1 102 ILE 102 102 102 ILE ILE A . n A 1 103 GLY 103 103 103 GLY GLY A . n A 1 104 ASN 104 104 104 ASN ASN A . n A 1 105 ALA 105 105 105 ALA ALA A . n A 1 106 MET 106 106 106 MET MET A . n A 1 107 GLY 107 107 107 GLY GLY A . n A 1 108 GLY 108 108 108 GLY GLY A . n A 1 109 THR 109 109 109 THR THR A . n A 1 110 THR 110 110 110 THR THR A . n A 1 111 ALA 111 111 111 ALA ALA A . n A 1 112 CYS 112 112 112 CYS CYS A . n A 1 113 GLY 113 113 113 GLY GLY A . n A 1 114 ALA 114 114 114 ALA ALA A . n A 1 115 ALA 115 115 115 ALA ALA A . n A 1 116 LEU 116 116 116 LEU LEU A . n A 1 117 LYS 117 117 117 LYS LYS A . n A 1 118 ALA 118 118 118 ALA ALA A . n A 1 119 PRO 119 119 119 PRO PRO A . n A 1 120 GLU 120 120 120 GLU GLU A . n A 1 121 LEU 121 121 121 LEU LEU A . n A 1 122 ILE 122 122 122 ILE ILE A . n A 1 123 ASP 123 123 123 ASP ASP A . n A 1 124 ARG 124 124 124 ARG ARG A . n A 1 125 LEU 125 125 125 LEU LEU A . n A 1 126 VAL 126 126 126 VAL VAL A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 MET 128 128 128 MET MET A . n A 1 129 GLY 129 129 129 GLY GLY A . n A 1 130 ALA 130 130 130 ALA ALA A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 VAL 132 132 132 VAL VAL A . n A 1 133 ASN 133 133 133 ASN ASN A . n A 1 134 ILE 134 134 134 ILE ILE A . n A 1 135 SER 135 135 135 SER SER A . n A 1 136 PRO 136 136 136 PRO PRO A . n A 1 137 ASP 137 137 137 ASP ASP A . n A 1 138 ASP 138 138 138 ASP ASP 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 ALA 141 141 141 ALA ALA A . n A 1 142 ASN 142 142 142 ASN ASN A . n A 1 143 ARG 143 143 143 ARG ARG A . n A 1 144 ASP 144 144 144 ASP ASP A . n A 1 145 ASP 145 145 145 ASP ASP A . n A 1 146 LEU 146 146 146 LEU LEU A . n A 1 147 ALA 147 147 147 ALA ALA A . n A 1 148 ALA 148 148 148 ALA ALA A . n A 1 149 VAL 149 149 149 VAL VAL A . n A 1 150 MET 150 150 150 MET MET A . n A 1 151 SER 151 151 151 SER SER A . n A 1 152 TYR 152 152 152 TYR TYR A . n A 1 153 ASP 153 153 153 ASP ASP A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 SER 155 155 155 SER SER A . n A 1 156 GLU 156 156 156 GLU GLU A . n A 1 157 GLU 157 157 157 GLU GLU A . n A 1 158 GLY 158 158 158 GLY GLY A . n A 1 159 MET 159 159 159 MET MET A . n A 1 160 ARG 160 160 160 ARG ARG A . n A 1 161 LYS 161 161 161 LYS LYS A . n A 1 162 ILE 162 162 162 ILE ILE A . n A 1 163 ILE 163 163 163 ILE ILE A . n A 1 164 ALA 164 164 164 ALA ALA A . n A 1 165 ALA 165 165 165 ALA ALA A . n A 1 166 LEU 166 166 166 LEU LEU A . n A 1 167 THR 167 167 167 THR THR A . n A 1 168 HIS 168 168 168 HIS HIS A . n A 1 169 SER 169 169 169 SER SER A . n A 1 170 TYR 170 170 170 TYR TYR A . n A 1 171 GLN 171 171 171 GLN GLN A . n A 1 172 PRO 172 172 172 PRO PRO A . n A 1 173 THR 173 173 173 THR THR A . n A 1 174 ASP 174 174 174 ASP ASP A . n A 1 175 ASP 175 175 175 ASP ASP A . n A 1 176 ILE 176 176 176 ILE ILE A . n A 1 177 VAL 177 177 177 VAL VAL A . n A 1 178 HIS 178 178 178 HIS HIS A . n A 1 179 TYR 179 179 179 TYR TYR A . n A 1 180 ARG 180 180 180 ARG ARG A . n A 1 181 HIS 181 181 181 HIS HIS A . n A 1 182 GLU 182 182 182 GLU GLU A . n A 1 183 ALA 183 183 183 ALA ALA A . n A 1 184 SER 184 184 184 SER SER A . n A 1 185 LEU 185 185 185 LEU LEU A . n A 1 186 ARG 186 186 186 ARG ARG A . n A 1 187 PRO 187 187 187 PRO PRO A . n A 1 188 THR 188 188 188 THR THR A . n A 1 189 THR 189 189 189 THR THR A . n A 1 190 THR 190 190 190 THR THR A . n A 1 191 ALA 191 191 191 ALA ALA A . n A 1 192 ALA 192 192 192 ALA ALA A . n A 1 193 TYR 193 193 193 TYR TYR A . n A 1 194 LYS 194 194 194 LYS LYS A . n A 1 195 ALA 195 195 195 ALA ALA A . n A 1 196 THR 196 196 196 THR THR A . n A 1 197 MET 197 197 197 MET MET A . n A 1 198 GLY 198 198 198 GLY GLY A . n A 1 199 TRP 199 199 199 TRP TRP A . n A 1 200 ALA 200 200 200 ALA ALA A . n A 1 201 LYS 201 201 201 LYS LYS A . n A 1 202 GLN 202 202 202 GLN GLN A . n A 1 203 ASN 203 203 203 ASN ASN A . n A 1 204 GLY 204 204 204 GLY GLY A . n A 1 205 LEU 205 205 205 LEU LEU A . n A 1 206 TYR 206 206 206 TYR TYR A . n A 1 207 TYR 207 207 207 TYR TYR A . n A 1 208 SER 208 208 208 SER SER A . n A 1 209 PRO 209 209 209 PRO PRO A . n A 1 210 GLU 210 210 210 GLU GLU A . n A 1 211 GLN 211 211 211 GLN GLN A . n A 1 212 LEU 212 212 212 LEU LEU A . n A 1 213 ALA 213 213 213 ALA ALA A . n A 1 214 SER 214 214 214 SER SER A . n A 1 215 LEU 215 215 215 LEU LEU A . n A 1 216 THR 216 216 216 THR THR A . n A 1 217 MET 217 217 217 MET MET A . n A 1 218 PRO 218 218 218 PRO PRO A . n A 1 219 VAL 219 219 219 VAL VAL A . n A 1 220 LEU 220 220 220 LEU LEU A . n A 1 221 VAL 221 221 221 VAL VAL A . n A 1 222 LEU 222 222 222 LEU LEU A . n A 1 223 GLY 223 223 223 GLY GLY A . n A 1 224 GLY 224 224 224 GLY GLY A . n A 1 225 LYS 225 225 225 LYS LYS A . n A 1 226 ASN 226 226 226 ASN ASN A . n A 1 227 ASP 227 227 227 ASP ASP A . n A 1 228 VAL 228 228 228 VAL VAL A . n A 1 229 MET 229 229 229 MET MET A . n A 1 230 VAL 230 230 230 VAL VAL A . n A 1 231 PRO 231 231 231 PRO PRO A . n A 1 232 VAL 232 232 232 VAL VAL A . n A 1 233 ARG 233 233 233 ARG ARG A . n A 1 234 LYS 234 234 234 LYS LYS A . n A 1 235 VAL 235 235 235 VAL VAL A . n A 1 236 ILE 236 236 236 ILE ILE A . n A 1 237 ASP 237 237 237 ASP ASP A . n A 1 238 GLN 238 238 238 GLN GLN A . n A 1 239 ILE 239 239 239 ILE ILE A . n A 1 240 LEU 240 240 240 LEU LEU A . n A 1 241 ALA 241 241 241 ALA ALA A . n A 1 242 ILE 242 242 242 ILE ILE A . n A 1 243 PRO 243 243 243 PRO PRO A . n A 1 244 GLN 244 244 244 GLN GLN A . n A 1 245 ALA 245 245 245 ALA ALA A . n A 1 246 ILE 246 246 246 ILE ILE A . n A 1 247 GLY 247 247 247 GLY GLY A . n A 1 248 HIS 248 248 248 HIS HIS A . n A 1 249 VAL 249 249 249 VAL VAL A . n A 1 250 PHE 250 250 250 PHE PHE A . n A 1 251 PRO 251 251 251 PRO PRO A . n A 1 252 ASN 252 252 252 ASN ASN A . n A 1 253 CYS 253 253 253 CYS CYS A . n A 1 254 GLY 254 254 254 GLY GLY A . n A 1 255 HIS 255 255 255 HIS HIS A . n A 1 256 TRP 256 256 256 TRP TRP A . n A 1 257 VAL 257 257 257 VAL VAL A . n A 1 258 MET 258 258 258 MET MET A . n A 1 259 ILE 259 259 259 ILE ILE A . n A 1 260 GLU 260 260 260 GLU GLU A . n A 1 261 TYR 261 261 261 TYR TYR A . n A 1 262 PRO 262 262 262 PRO PRO A . n A 1 263 GLU 263 263 263 GLU GLU A . n A 1 264 GLU 264 264 264 GLU GLU A . n A 1 265 PHE 265 265 265 PHE PHE A . n A 1 266 CYS 266 266 266 CYS CYS A . n A 1 267 THR 267 267 267 THR THR A . n A 1 268 GLN 268 268 268 GLN GLN A . n A 1 269 THR 269 269 269 THR THR A . n A 1 270 LEU 270 270 270 LEU LEU A . n A 1 271 HIS 271 271 271 HIS HIS A . n A 1 272 PHE 272 272 272 PHE PHE A . n A 1 273 PHE 273 273 273 PHE PHE A . n A 1 274 GLY 274 274 274 GLY GLY A . n A 1 275 LYS 275 275 275 LYS LYS A . n A 1 276 LEU 276 276 276 LEU LEU A . n A 1 277 ASP 277 277 ? ? ? 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 HPK 1 301 289 HPK HPK A . C 3 HOH 1 401 1 HOH HOH A . C 3 HOH 2 402 2 HOH HOH A . C 3 HOH 3 403 3 HOH HOH A . C 3 HOH 4 404 4 HOH HOH A . C 3 HOH 5 405 5 HOH HOH A . C 3 HOH 6 406 6 HOH HOH A . C 3 HOH 7 407 7 HOH HOH A . C 3 HOH 8 408 8 HOH HOH A . C 3 HOH 9 409 9 HOH HOH A . C 3 HOH 10 410 10 HOH HOH A . C 3 HOH 11 411 11 HOH HOH A . C 3 HOH 12 412 12 HOH HOH A . C 3 HOH 13 413 13 HOH HOH A . C 3 HOH 14 414 14 HOH HOH A . C 3 HOH 15 415 15 HOH HOH A . C 3 HOH 16 416 16 HOH HOH A . C 3 HOH 17 417 17 HOH HOH A . C 3 HOH 18 418 18 HOH HOH A . C 3 HOH 19 419 19 HOH HOH A . C 3 HOH 20 420 20 HOH HOH A . C 3 HOH 21 421 21 HOH HOH A . C 3 HOH 22 422 22 HOH HOH A . C 3 HOH 23 423 23 HOH HOH A . C 3 HOH 24 424 24 HOH HOH A . C 3 HOH 25 425 25 HOH HOH A . C 3 HOH 26 426 26 HOH HOH A . C 3 HOH 27 427 27 HOH HOH A . C 3 HOH 28 428 28 HOH HOH A . C 3 HOH 29 429 29 HOH HOH A . C 3 HOH 30 430 30 HOH HOH A . C 3 HOH 31 431 31 HOH HOH A . C 3 HOH 32 432 32 HOH HOH A . C 3 HOH 33 433 33 HOH HOH A . C 3 HOH 34 434 34 HOH HOH A . C 3 HOH 35 435 35 HOH HOH A . C 3 HOH 36 436 36 HOH HOH A . C 3 HOH 37 437 37 HOH HOH A . C 3 HOH 38 438 38 HOH HOH A . C 3 HOH 39 439 39 HOH HOH A . C 3 HOH 40 440 40 HOH HOH A . C 3 HOH 41 441 41 HOH HOH A . C 3 HOH 42 442 42 HOH HOH A . C 3 HOH 43 443 43 HOH HOH A . C 3 HOH 44 444 44 HOH HOH A . C 3 HOH 45 445 45 HOH HOH A . C 3 HOH 46 446 46 HOH HOH A . C 3 HOH 47 447 47 HOH HOH A . C 3 HOH 48 448 48 HOH HOH A . C 3 HOH 49 449 49 HOH HOH A . C 3 HOH 50 450 50 HOH HOH A . C 3 HOH 51 451 51 HOH HOH A . C 3 HOH 52 452 52 HOH HOH A . C 3 HOH 53 453 53 HOH HOH A . C 3 HOH 54 454 54 HOH HOH A . C 3 HOH 55 455 55 HOH HOH A . C 3 HOH 56 456 56 HOH HOH A . C 3 HOH 57 457 57 HOH HOH A . C 3 HOH 58 458 58 HOH HOH A . C 3 HOH 59 459 59 HOH HOH A . C 3 HOH 60 460 60 HOH HOH A . C 3 HOH 61 461 61 HOH HOH A . C 3 HOH 62 462 62 HOH HOH A . C 3 HOH 63 463 63 HOH HOH A . C 3 HOH 64 464 64 HOH HOH A . C 3 HOH 65 465 65 HOH HOH A . C 3 HOH 66 466 66 HOH HOH A . C 3 HOH 67 467 67 HOH HOH A . C 3 HOH 68 468 68 HOH HOH A . C 3 HOH 69 469 69 HOH HOH A . C 3 HOH 70 470 70 HOH HOH A . C 3 HOH 71 471 71 HOH HOH A . C 3 HOH 72 472 72 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_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' 10_555 -y,-x,-z+1/6 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 56.5420000000 # 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 2013-10-09 2 'Structure model' 1 1 2013-11-06 3 'Structure model' 1 2 2017-11-15 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _pdbx_phasing_MR.entry_id 4LYE _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor 44.210 _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.330 _pdbx_phasing_MR.d_res_low_rotation 21.130 _pdbx_phasing_MR.d_res_high_translation 2.330 _pdbx_phasing_MR.d_res_low_translation 21.130 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 PHASER 2.1.4 'Thu Nov 13 10:53:32 2008' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # loop_ _pdbx_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 ASP A 13 ? ? 32.41 59.94 2 1 ALA A 70 ? ? -118.18 79.19 3 1 ALA A 105 ? ? 51.11 -121.75 4 1 ASN A 133 ? ? -146.41 32.89 # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id ASP _pdbx_unobs_or_zero_occ_residues.auth_seq_id 277 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id ASP _pdbx_unobs_or_zero_occ_residues.label_seq_id 277 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE' HPK 3 water HOH #