data_3VQW # _entry.id 3VQW # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3VQW RCSB RCSB095388 WWPDB D_1000095388 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2e3c . unspecified PDB 2zcd . unspecified PDB 2zce . unspecified PDB 2zin . unspecified PDB 2zio . unspecified PDB 3vqv . unspecified PDB 3vqx . unspecified PDB 3vqy . unspecified TargetTrack RSGI-trt001000322.9 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3VQW _pdbx_database_status.recvd_initial_deposition_date 2012-04-01 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yanagisawa, T.' 1 'Sumida, T.' 2 'Ishii, R.' 3 'Yokoyama, S.' 4 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 5 # _citation.id primary _citation.title ;A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 69 _citation.page_first 5 _citation.page_last 15 _citation.year 2013 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23275158 _citation.pdbx_database_id_DOI 10.1107/S0907444912039881 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Yanagisawa, T.' 1 primary 'Sumida, T.' 2 primary 'Ishii, R.' 3 primary 'Yokoyama, S.' 4 # _cell.entry_id 3VQW _cell.length_a 105.091 _cell.length_b 105.091 _cell.length_c 70.629 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3VQW _symmetry.space_group_name_H-M 'P 64' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _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 'Pyrrolysine--tRNA ligase' 33719.324 1 6.1.1.26 E444G ? ? 2 non-polymer syn 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 506.196 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 water nat water 18.015 143 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Pyrrolysyl-tRNA synthetase, PylRS' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;(MSE)GSSHHHHHHSSGLVPRGSH(MSE)ASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIY AEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIER(MSE)GIDNDTELSKQIFRVDKNFCLRP(MSE)LAPNLYN YLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFT(MSE)LNFCQ(MSE)GSGCTRENLESIITDFLNHLGIDFKIVGD SC(MSE)VYGDTLDV(MSE)HGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGIS TNL ; _entity_poly.pdbx_seq_one_letter_code_can ;MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier RSGI-trt001000322.9 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 GLY n 1 3 SER n 1 4 SER n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 HIS n 1 11 SER n 1 12 SER n 1 13 GLY n 1 14 LEU n 1 15 VAL n 1 16 PRO n 1 17 ARG n 1 18 GLY n 1 19 SER n 1 20 HIS n 1 21 MSE n 1 22 ALA n 1 23 SER n 1 24 ALA n 1 25 PRO n 1 26 ALA n 1 27 LEU n 1 28 THR n 1 29 LYS n 1 30 SER n 1 31 GLN n 1 32 THR n 1 33 ASP n 1 34 ARG n 1 35 LEU n 1 36 GLU n 1 37 VAL n 1 38 LEU n 1 39 LEU n 1 40 ASN n 1 41 PRO n 1 42 LYS n 1 43 ASP n 1 44 GLU n 1 45 ILE n 1 46 SER n 1 47 LEU n 1 48 ASN n 1 49 SER n 1 50 GLY n 1 51 LYS n 1 52 PRO n 1 53 PHE n 1 54 ARG n 1 55 GLU n 1 56 LEU n 1 57 GLU n 1 58 SER n 1 59 GLU n 1 60 LEU n 1 61 LEU n 1 62 SER n 1 63 ARG n 1 64 ARG n 1 65 LYS n 1 66 LYS n 1 67 ASP n 1 68 LEU n 1 69 GLN n 1 70 GLN n 1 71 ILE n 1 72 TYR n 1 73 ALA n 1 74 GLU n 1 75 GLU n 1 76 ARG n 1 77 GLU n 1 78 ASN n 1 79 TYR n 1 80 LEU n 1 81 GLY n 1 82 LYS n 1 83 LEU n 1 84 GLU n 1 85 ARG n 1 86 GLU n 1 87 ILE n 1 88 THR n 1 89 ARG n 1 90 PHE n 1 91 PHE n 1 92 VAL n 1 93 ASP n 1 94 ARG n 1 95 GLY n 1 96 PHE n 1 97 LEU n 1 98 GLU n 1 99 ILE n 1 100 LYS n 1 101 SER n 1 102 PRO n 1 103 ILE n 1 104 LEU n 1 105 ILE n 1 106 PRO n 1 107 LEU n 1 108 GLU n 1 109 TYR n 1 110 ILE n 1 111 GLU n 1 112 ARG n 1 113 MSE n 1 114 GLY n 1 115 ILE n 1 116 ASP n 1 117 ASN n 1 118 ASP n 1 119 THR n 1 120 GLU n 1 121 LEU n 1 122 SER n 1 123 LYS n 1 124 GLN n 1 125 ILE n 1 126 PHE n 1 127 ARG n 1 128 VAL n 1 129 ASP n 1 130 LYS n 1 131 ASN n 1 132 PHE n 1 133 CYS n 1 134 LEU n 1 135 ARG n 1 136 PRO n 1 137 MSE n 1 138 LEU n 1 139 ALA n 1 140 PRO n 1 141 ASN n 1 142 LEU n 1 143 TYR n 1 144 ASN n 1 145 TYR n 1 146 LEU n 1 147 ARG n 1 148 LYS n 1 149 LEU n 1 150 ASP n 1 151 ARG n 1 152 ALA n 1 153 LEU n 1 154 PRO n 1 155 ASP n 1 156 PRO n 1 157 ILE n 1 158 LYS n 1 159 ILE n 1 160 PHE n 1 161 GLU n 1 162 ILE n 1 163 GLY n 1 164 PRO n 1 165 CYS n 1 166 TYR n 1 167 ARG n 1 168 LYS n 1 169 GLU n 1 170 SER n 1 171 ASP n 1 172 GLY n 1 173 LYS n 1 174 GLU n 1 175 HIS n 1 176 LEU n 1 177 GLU n 1 178 GLU n 1 179 PHE n 1 180 THR n 1 181 MSE n 1 182 LEU n 1 183 ASN n 1 184 PHE n 1 185 CYS n 1 186 GLN n 1 187 MSE n 1 188 GLY n 1 189 SER n 1 190 GLY n 1 191 CYS n 1 192 THR n 1 193 ARG n 1 194 GLU n 1 195 ASN n 1 196 LEU n 1 197 GLU n 1 198 SER n 1 199 ILE n 1 200 ILE n 1 201 THR n 1 202 ASP n 1 203 PHE n 1 204 LEU n 1 205 ASN n 1 206 HIS n 1 207 LEU n 1 208 GLY n 1 209 ILE n 1 210 ASP n 1 211 PHE n 1 212 LYS n 1 213 ILE n 1 214 VAL n 1 215 GLY n 1 216 ASP n 1 217 SER n 1 218 CYS n 1 219 MSE n 1 220 VAL n 1 221 TYR n 1 222 GLY n 1 223 ASP n 1 224 THR n 1 225 LEU n 1 226 ASP n 1 227 VAL n 1 228 MSE n 1 229 HIS n 1 230 GLY n 1 231 ASP n 1 232 LEU n 1 233 GLU n 1 234 LEU n 1 235 SER n 1 236 SER n 1 237 ALA n 1 238 VAL n 1 239 VAL n 1 240 GLY n 1 241 PRO n 1 242 ILE n 1 243 PRO n 1 244 LEU n 1 245 ASP n 1 246 ARG n 1 247 GLU n 1 248 TRP n 1 249 GLY n 1 250 ILE n 1 251 ASP n 1 252 LYS n 1 253 PRO n 1 254 TRP n 1 255 ILE n 1 256 GLY n 1 257 ALA n 1 258 GLY n 1 259 PHE n 1 260 GLY n 1 261 LEU n 1 262 GLU n 1 263 ARG n 1 264 LEU n 1 265 LEU n 1 266 LYS n 1 267 VAL n 1 268 LYS n 1 269 HIS n 1 270 ASP n 1 271 PHE n 1 272 LYS n 1 273 ASN n 1 274 ILE n 1 275 LYS n 1 276 ARG n 1 277 ALA n 1 278 ALA n 1 279 ARG n 1 280 SER n 1 281 GLY n 1 282 SER n 1 283 TYR n 1 284 TYR n 1 285 ASN n 1 286 GLY n 1 287 ILE n 1 288 SER n 1 289 THR n 1 290 ASN n 1 291 LEU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene pylS _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain JCM9314 _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 'Methanosarcina mazei' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2209 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3) codon plus' _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 pET28c _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3VQW _struct_ref.pdbx_db_accession 3VQW _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3VQW _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 291 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3VQW _struct_ref_seq.db_align_beg 164 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 454 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 164 _struct_ref_seq.pdbx_auth_seq_align_end 454 # 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 ANP non-polymer . 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' ? 'C10 H17 N6 O12 P3' 506.196 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3VQW _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.34 _exptl_crystal.density_percent_sol 63.16 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.8 _exptl_crystal_grow.pdbx_details 'Na/Cacodylate, NaCl, MgSO4, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RIGAKU JUPITER 210' _diffrn_detector.pdbx_collection_date 2004-03-04 _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 ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9791 1.0 2 0.9794 1.0 3 0.9840 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL26B1' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL26B1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9791, 0.9794, 0.9840' # _reflns.entry_id 3VQW _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.4 _reflns.number_obs 17400 _reflns.number_all ? _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.090 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 13.2 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.4 _reflns_shell.d_res_low 2.44 _reflns_shell.percent_possible_all 96.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.411 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3VQW _refine.ls_number_reflns_obs 17347 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 2093308.17 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 42.16 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_obs 0.200 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.200 _refine.ls_R_factor_R_free 0.270 _refine.ls_R_factor_R_free_error 0.006 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.9 _refine.ls_number_reflns_R_free 1726 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 45.7 _refine.aniso_B[1][1] -5.12 _refine.aniso_B[2][2] -5.12 _refine.aniso_B[3][3] 10.24 _refine.aniso_B[1][2] 4.72 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.293082 _refine.solvent_model_param_bsol 42.2699 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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_analyze.entry_id 3VQW _refine_analyze.Luzzati_coordinate_error_obs 0.28 _refine_analyze.Luzzati_sigma_a_obs 0.55 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.39 _refine_analyze.Luzzati_sigma_a_free 0.66 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2095 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 33 _refine_hist.number_atoms_solvent 143 _refine_hist.number_atoms_total 2271 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 42.16 # 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_restraint_function _refine_ls_restr.pdbx_refine_id c_bond_d 0.010 ? ? ? ? 'X-RAY DIFFRACTION' c_angle_deg 1.6 ? ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d 24.0 ? ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d 1.88 ? ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it 5.71 1.50 ? ? ? 'X-RAY DIFFRACTION' c_mcangle_it 7.92 2.00 ? ? ? 'X-RAY DIFFRACTION' c_scbond_it 9.35 2.00 ? ? ? 'X-RAY DIFFRACTION' c_scangle_it 11.53 2.50 ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.40 _refine_ls_shell.d_res_low 2.55 _refine_ls_shell.number_reflns_R_work 2494 _refine_ls_shell.R_factor_R_work 0.370 _refine_ls_shell.percent_reflns_obs 95.9 _refine_ls_shell.R_factor_R_free 0.409 _refine_ls_shell.R_factor_R_free_error 0.024 _refine_ls_shell.percent_reflns_R_free 10.3 _refine_ls_shell.number_reflns_R_free 285 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' 4 AMPPNP.param AMPPNP.top # _struct.entry_id 3VQW _struct.title 'Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase' _struct.pdbx_descriptor 'Pyrrolysine--tRNA ligase (E.C.6.1.1.26)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VQW _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text ;Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, aminoacyl-tRNA synthetase, pyrrolysyl-tRNA synthetase, AMPPNP, LIGASE ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? # _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 THR A 28 ? LEU A 38 ? THR A 191 LEU A 201 1 ? 11 HELX_P HELX_P2 2 PRO A 52 ? GLU A 74 ? PRO A 215 GLU A 237 1 ? 23 HELX_P HELX_P3 3 ASN A 78 ? ARG A 94 ? ASN A 241 ARG A 257 1 ? 17 HELX_P HELX_P4 4 LEU A 107 ? ARG A 112 ? LEU A 270 ARG A 275 1 ? 6 HELX_P HELX_P5 5 THR A 119 ? LYS A 123 ? THR A 282 LYS A 286 5 ? 5 HELX_P HELX_P6 6 LEU A 138 ? ARG A 151 ? LEU A 301 ARG A 314 1 ? 14 HELX_P HELX_P7 7 THR A 192 ? GLY A 208 ? THR A 355 GLY A 371 1 ? 17 HELX_P HELX_P8 8 ILE A 242 ? GLY A 249 ? ILE A 405 GLY A 412 5 ? 8 HELX_P HELX_P9 9 LEU A 261 ? HIS A 269 ? LEU A 424 HIS A 432 1 ? 9 HELX_P HELX_P10 10 ASN A 273 ? ALA A 278 ? ASN A 436 ALA A 441 5 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A ARG 112 C ? ? ? 1_555 A MSE 113 N ? ? A ARG 275 A MSE 276 1_555 ? ? ? ? ? ? ? 1.327 ? covale2 covale ? ? A MSE 113 C ? ? ? 1_555 A GLY 114 N ? ? A MSE 276 A GLY 277 1_555 ? ? ? ? ? ? ? 1.331 ? covale3 covale ? ? A PRO 136 C ? ? ? 1_555 A MSE 137 N ? ? A PRO 299 A MSE 300 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale ? ? A MSE 137 C ? ? ? 1_555 A LEU 138 N ? ? A MSE 300 A LEU 301 1_555 ? ? ? ? ? ? ? 1.335 ? covale5 covale ? ? A THR 180 C ? ? ? 1_555 A MSE 181 N ? ? A THR 343 A MSE 344 1_555 ? ? ? ? ? ? ? 1.327 ? covale6 covale ? ? A MSE 181 C ? ? ? 1_555 A LEU 182 N ? ? A MSE 344 A LEU 345 1_555 ? ? ? ? ? ? ? 1.327 ? covale7 covale ? ? A GLN 186 C ? ? ? 1_555 A MSE 187 N ? ? A GLN 349 A MSE 350 1_555 ? ? ? ? ? ? ? 1.332 ? covale8 covale ? ? A MSE 187 C ? ? ? 1_555 A GLY 188 N ? ? A MSE 350 A GLY 351 1_555 ? ? ? ? ? ? ? 1.346 ? covale9 covale ? ? A VAL 227 C ? ? ? 1_555 A MSE 228 N ? ? A VAL 390 A MSE 391 1_555 ? ? ? ? ? ? ? 1.331 ? covale10 covale ? ? A MSE 228 C ? ? ? 1_555 A HIS 229 N ? ? A MSE 391 A HIS 392 1_555 ? ? ? ? ? ? ? 1.334 ? metalc1 metalc ? ? B ANP . O2B ? ? ? 1_555 D MG . MG ? ? A ANP 501 A MG 503 1_555 ? ? ? ? ? ? ? 2.285 ? metalc2 metalc ? ? A SER 236 OG ? ? ? 1_555 D MG . MG ? ? A SER 399 A MG 503 1_555 ? ? ? ? ? ? ? 2.394 ? metalc3 metalc ? ? B ANP . O1B ? ? ? 1_555 C MG . MG ? ? A ANP 501 A MG 502 1_555 ? ? ? ? ? ? ? 2.512 ? metalc4 metalc ? ? B ANP . O1A ? ? ? 1_555 D MG . MG ? ? A ANP 501 A MG 503 1_555 ? ? ? ? ? ? ? 2.565 ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 502 A HOH 734 1_555 ? ? ? ? ? ? ? 2.628 ? metalc6 metalc ? ? B ANP . O1G ? ? ? 1_555 C MG . MG ? ? A ANP 501 A MG 502 1_555 ? ? ? ? ? ? ? 2.637 ? metalc7 metalc ? ? A GLU 233 OE1 ? ? ? 1_555 D MG . MG ? ? A GLU 396 A MG 503 1_555 ? ? ? ? ? ? ? 2.770 ? metalc8 metalc ? ? A GLU 233 OE2 ? ? ? 1_555 D MG . MG ? ? A GLU 396 A MG 503 1_555 ? ? ? ? ? ? ? 2.782 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # 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 ASP 155 A . ? ASP 318 A PRO 156 A ? PRO 319 A 1 0.00 2 GLY 240 A . ? GLY 403 A PRO 241 A ? PRO 404 A 1 0.19 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 7 ? B ? 3 ? C ? 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 ? parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel C 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 LEU A 97 ? ILE A 99 ? LEU A 260 ILE A 262 A 2 ILE A 157 ? TYR A 166 ? ILE A 320 TYR A 329 A 3 GLU A 178 ? MSE A 187 ? GLU A 341 MSE A 350 A 4 TRP A 254 ? GLY A 260 ? TRP A 417 GLY A 423 A 5 LEU A 232 ? VAL A 239 ? LEU A 395 VAL A 402 A 6 ASP A 223 ? HIS A 229 ? ASP A 386 HIS A 392 A 7 LYS A 212 ? ILE A 213 ? LYS A 375 ILE A 376 B 1 LEU A 104 ? PRO A 106 ? LEU A 267 PRO A 269 B 2 PHE A 132 ? LEU A 134 ? PHE A 295 LEU A 297 B 3 ARG A 127 ? VAL A 128 ? ARG A 290 VAL A 291 C 1 TYR A 283 ? TYR A 284 ? TYR A 446 TYR A 447 C 2 ILE A 287 ? SER A 288 ? ILE A 450 SER A 451 # 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 ILE A 99 ? N ILE A 262 O PHE A 160 ? O PHE A 323 A 2 3 N ILE A 157 ? N ILE A 320 O MSE A 187 ? O MSE A 350 A 3 4 N LEU A 182 ? N LEU A 345 O PHE A 259 ? O PHE A 422 A 4 5 O GLY A 256 ? O GLY A 419 N VAL A 238 ? N VAL A 401 A 5 6 O SER A 235 ? O SER A 398 N VAL A 227 ? N VAL A 390 A 6 7 O MSE A 228 ? O MSE A 391 N LYS A 212 ? N LYS A 375 B 1 2 N ILE A 105 ? N ILE A 268 O CYS A 133 ? O CYS A 296 B 2 3 O PHE A 132 ? O PHE A 295 N VAL A 128 ? N VAL A 291 C 1 2 N TYR A 284 ? N TYR A 447 O ILE A 287 ? O ILE A 450 # 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 ? ? ? ? 20 'BINDING SITE FOR RESIDUE ANP A 501' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MG A 502' AC3 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MG A 503' # 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 20 ARG A 167 ? ARG A 330 . ? 1_555 ? 2 AC1 20 GLU A 169 ? GLU A 332 . ? 1_555 ? 3 AC1 20 HIS A 175 ? HIS A 338 . ? 1_555 ? 4 AC1 20 LEU A 176 ? LEU A 339 . ? 1_555 ? 5 AC1 20 PHE A 179 ? PHE A 342 . ? 1_555 ? 6 AC1 20 MSE A 181 ? MSE A 344 . ? 1_555 ? 7 AC1 20 GLU A 233 ? GLU A 396 . ? 1_555 ? 8 AC1 20 LEU A 234 ? LEU A 397 . ? 1_555 ? 9 AC1 20 SER A 236 ? SER A 399 . ? 1_555 ? 10 AC1 20 GLY A 258 ? GLY A 421 . ? 1_555 ? 11 AC1 20 PHE A 259 ? PHE A 422 . ? 1_555 ? 12 AC1 20 GLY A 260 ? GLY A 423 . ? 1_555 ? 13 AC1 20 ARG A 263 ? ARG A 426 . ? 1_555 ? 14 AC1 20 MG C . ? MG A 502 . ? 1_555 ? 15 AC1 20 MG D . ? MG A 503 . ? 1_555 ? 16 AC1 20 HOH E . ? HOH A 602 . ? 1_555 ? 17 AC1 20 HOH E . ? HOH A 641 . ? 1_555 ? 18 AC1 20 HOH E . ? HOH A 645 . ? 1_555 ? 19 AC1 20 HOH E . ? HOH A 648 . ? 1_555 ? 20 AC1 20 HOH E . ? HOH A 734 . ? 1_555 ? 21 AC2 3 GLU A 120 ? GLU A 283 . ? 1_555 ? 22 AC2 3 ANP B . ? ANP A 501 . ? 1_555 ? 23 AC2 3 HOH E . ? HOH A 734 . ? 1_555 ? 24 AC3 3 GLU A 233 ? GLU A 396 . ? 1_555 ? 25 AC3 3 SER A 236 ? SER A 399 . ? 1_555 ? 26 AC3 3 ANP B . ? ANP A 501 . ? 1_555 ? # _database_PDB_matrix.entry_id 3VQW _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 3VQW _atom_sites.fract_transf_matrix[1][1] 0.009516 _atom_sites.fract_transf_matrix[1][2] 0.005494 _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] 0.010988 _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] 0.014158 _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 MG N O P S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MSE 1 164 ? ? ? A . n A 1 2 GLY 2 165 ? ? ? A . n A 1 3 SER 3 166 ? ? ? A . n A 1 4 SER 4 167 ? ? ? A . n A 1 5 HIS 5 168 ? ? ? A . n A 1 6 HIS 6 169 ? ? ? A . n A 1 7 HIS 7 170 ? ? ? A . n A 1 8 HIS 8 171 ? ? ? A . n A 1 9 HIS 9 172 ? ? ? A . n A 1 10 HIS 10 173 ? ? ? A . n A 1 11 SER 11 174 ? ? ? A . n A 1 12 SER 12 175 ? ? ? A . n A 1 13 GLY 13 176 ? ? ? A . n A 1 14 LEU 14 177 ? ? ? A . n A 1 15 VAL 15 178 ? ? ? A . n A 1 16 PRO 16 179 ? ? ? A . n A 1 17 ARG 17 180 ? ? ? A . n A 1 18 GLY 18 181 ? ? ? A . n A 1 19 SER 19 182 ? ? ? A . n A 1 20 HIS 20 183 ? ? ? A . n A 1 21 MSE 21 184 ? ? ? A . n A 1 22 ALA 22 185 ? ? ? A . n A 1 23 SER 23 186 ? ? ? A . n A 1 24 ALA 24 187 ? ? ? A . n A 1 25 PRO 25 188 188 PRO PRO A . n A 1 26 ALA 26 189 189 ALA ALA A . n A 1 27 LEU 27 190 190 LEU LEU A . n A 1 28 THR 28 191 191 THR THR A . n A 1 29 LYS 29 192 192 LYS LYS A . n A 1 30 SER 30 193 193 SER SER A . n A 1 31 GLN 31 194 194 GLN GLN A . n A 1 32 THR 32 195 195 THR THR A . n A 1 33 ASP 33 196 196 ASP ASP A . n A 1 34 ARG 34 197 197 ARG ARG A . n A 1 35 LEU 35 198 198 LEU LEU A . n A 1 36 GLU 36 199 199 GLU GLU A . n A 1 37 VAL 37 200 200 VAL VAL A . n A 1 38 LEU 38 201 201 LEU LEU A . n A 1 39 LEU 39 202 202 LEU LEU A . n A 1 40 ASN 40 203 203 ASN ASN A . n A 1 41 PRO 41 204 204 PRO PRO A . n A 1 42 LYS 42 205 205 LYS LYS A . n A 1 43 ASP 43 206 206 ASP ASP A . n A 1 44 GLU 44 207 207 GLU GLU A . n A 1 45 ILE 45 208 ? ? ? A . n A 1 46 SER 46 209 ? ? ? A . n A 1 47 LEU 47 210 ? ? ? A . n A 1 48 ASN 48 211 ? ? ? A . n A 1 49 SER 49 212 212 SER SER A . n A 1 50 GLY 50 213 213 GLY GLY A . n A 1 51 LYS 51 214 214 LYS LYS A . n A 1 52 PRO 52 215 215 PRO PRO A . n A 1 53 PHE 53 216 216 PHE PHE A . n A 1 54 ARG 54 217 217 ARG ARG A . n A 1 55 GLU 55 218 218 GLU GLU A . n A 1 56 LEU 56 219 219 LEU LEU A . n A 1 57 GLU 57 220 220 GLU GLU A . n A 1 58 SER 58 221 221 SER SER A . n A 1 59 GLU 59 222 222 GLU GLU A . n A 1 60 LEU 60 223 223 LEU LEU A . n A 1 61 LEU 61 224 224 LEU LEU A . n A 1 62 SER 62 225 225 SER SER A . n A 1 63 ARG 63 226 226 ARG ARG A . n A 1 64 ARG 64 227 227 ARG ARG A . n A 1 65 LYS 65 228 228 LYS LYS A . n A 1 66 LYS 66 229 229 LYS LYS A . n A 1 67 ASP 67 230 230 ASP ASP A . n A 1 68 LEU 68 231 231 LEU LEU A . n A 1 69 GLN 69 232 232 GLN GLN A . n A 1 70 GLN 70 233 233 GLN GLN A . n A 1 71 ILE 71 234 234 ILE ILE A . n A 1 72 TYR 72 235 235 TYR TYR A . n A 1 73 ALA 73 236 236 ALA ALA A . n A 1 74 GLU 74 237 237 GLU GLU A . n A 1 75 GLU 75 238 238 GLU GLU A . n A 1 76 ARG 76 239 239 ARG ARG A . n A 1 77 GLU 77 240 240 GLU GLU A . n A 1 78 ASN 78 241 241 ASN ASN A . n A 1 79 TYR 79 242 242 TYR TYR A . n A 1 80 LEU 80 243 243 LEU LEU A . n A 1 81 GLY 81 244 244 GLY GLY A . n A 1 82 LYS 82 245 245 LYS LYS A . n A 1 83 LEU 83 246 246 LEU LEU A . n A 1 84 GLU 84 247 247 GLU GLU A . n A 1 85 ARG 85 248 248 ARG ARG A . n A 1 86 GLU 86 249 249 GLU GLU A . n A 1 87 ILE 87 250 250 ILE ILE A . n A 1 88 THR 88 251 251 THR THR A . n A 1 89 ARG 89 252 252 ARG ARG A . n A 1 90 PHE 90 253 253 PHE PHE A . n A 1 91 PHE 91 254 254 PHE PHE A . n A 1 92 VAL 92 255 255 VAL VAL A . n A 1 93 ASP 93 256 256 ASP ASP A . n A 1 94 ARG 94 257 257 ARG ARG A . n A 1 95 GLY 95 258 258 GLY GLY A . n A 1 96 PHE 96 259 259 PHE PHE A . n A 1 97 LEU 97 260 260 LEU LEU A . n A 1 98 GLU 98 261 261 GLU GLU A . n A 1 99 ILE 99 262 262 ILE ILE A . n A 1 100 LYS 100 263 263 LYS LYS A . n A 1 101 SER 101 264 264 SER SER A . n A 1 102 PRO 102 265 265 PRO PRO A . n A 1 103 ILE 103 266 266 ILE ILE A . n A 1 104 LEU 104 267 267 LEU LEU A . n A 1 105 ILE 105 268 268 ILE ILE A . n A 1 106 PRO 106 269 269 PRO PRO A . n A 1 107 LEU 107 270 270 LEU LEU A . n A 1 108 GLU 108 271 271 GLU GLU A . n A 1 109 TYR 109 272 272 TYR TYR A . n A 1 110 ILE 110 273 273 ILE ILE A . n A 1 111 GLU 111 274 274 GLU GLU A . n A 1 112 ARG 112 275 275 ARG ARG A . n A 1 113 MSE 113 276 276 MSE MSE A . n A 1 114 GLY 114 277 277 GLY GLY A . n A 1 115 ILE 115 278 278 ILE ILE A . n A 1 116 ASP 116 279 279 ASP ASP A . n A 1 117 ASN 117 280 280 ASN ASN A . n A 1 118 ASP 118 281 281 ASP ASP A . n A 1 119 THR 119 282 282 THR THR A . n A 1 120 GLU 120 283 283 GLU GLU A . n A 1 121 LEU 121 284 284 LEU LEU A . n A 1 122 SER 122 285 285 SER SER A . n A 1 123 LYS 123 286 286 LYS LYS A . n A 1 124 GLN 124 287 287 GLN GLN A . n A 1 125 ILE 125 288 288 ILE ILE A . n A 1 126 PHE 126 289 289 PHE PHE A . n A 1 127 ARG 127 290 290 ARG ARG A . n A 1 128 VAL 128 291 291 VAL VAL A . n A 1 129 ASP 129 292 292 ASP ASP A . n A 1 130 LYS 130 293 293 LYS LYS A . n A 1 131 ASN 131 294 294 ASN ASN A . n A 1 132 PHE 132 295 295 PHE PHE A . n A 1 133 CYS 133 296 296 CYS CYS A . n A 1 134 LEU 134 297 297 LEU LEU A . n A 1 135 ARG 135 298 298 ARG ARG A . n A 1 136 PRO 136 299 299 PRO PRO A . n A 1 137 MSE 137 300 300 MSE MSE A . n A 1 138 LEU 138 301 301 LEU LEU A . n A 1 139 ALA 139 302 302 ALA ALA A . n A 1 140 PRO 140 303 303 PRO PRO A . n A 1 141 ASN 141 304 304 ASN ASN A . n A 1 142 LEU 142 305 305 LEU LEU A . n A 1 143 TYR 143 306 306 TYR TYR A . n A 1 144 ASN 144 307 307 ASN ASN A . n A 1 145 TYR 145 308 308 TYR TYR A . n A 1 146 LEU 146 309 309 LEU LEU A . n A 1 147 ARG 147 310 310 ARG ARG A . n A 1 148 LYS 148 311 311 LYS LYS A . n A 1 149 LEU 149 312 312 LEU LEU A . n A 1 150 ASP 150 313 313 ASP ASP A . n A 1 151 ARG 151 314 314 ARG ARG A . n A 1 152 ALA 152 315 315 ALA ALA A . n A 1 153 LEU 153 316 316 LEU LEU A . n A 1 154 PRO 154 317 317 PRO PRO A . n A 1 155 ASP 155 318 318 ASP ASP A . n A 1 156 PRO 156 319 319 PRO PRO A . n A 1 157 ILE 157 320 320 ILE ILE A . n A 1 158 LYS 158 321 321 LYS LYS A . n A 1 159 ILE 159 322 322 ILE ILE A . n A 1 160 PHE 160 323 323 PHE PHE A . n A 1 161 GLU 161 324 324 GLU GLU A . n A 1 162 ILE 162 325 325 ILE ILE A . n A 1 163 GLY 163 326 326 GLY GLY A . n A 1 164 PRO 164 327 327 PRO PRO A . n A 1 165 CYS 165 328 328 CYS CYS A . n A 1 166 TYR 166 329 329 TYR TYR A . n A 1 167 ARG 167 330 330 ARG ARG A . n A 1 168 LYS 168 331 331 LYS LYS A . n A 1 169 GLU 169 332 332 GLU GLU A . n A 1 170 SER 170 333 333 SER SER A . n A 1 171 ASP 171 334 334 ASP ASP A . n A 1 172 GLY 172 335 335 GLY GLY A . n A 1 173 LYS 173 336 336 LYS LYS A . n A 1 174 GLU 174 337 337 GLU GLU A . n A 1 175 HIS 175 338 338 HIS HIS A . n A 1 176 LEU 176 339 339 LEU LEU A . n A 1 177 GLU 177 340 340 GLU GLU A . n A 1 178 GLU 178 341 341 GLU GLU A . n A 1 179 PHE 179 342 342 PHE PHE A . n A 1 180 THR 180 343 343 THR THR A . n A 1 181 MSE 181 344 344 MSE MSE A . n A 1 182 LEU 182 345 345 LEU LEU A . n A 1 183 ASN 183 346 346 ASN ASN A . n A 1 184 PHE 184 347 347 PHE PHE A . n A 1 185 CYS 185 348 348 CYS CYS A . n A 1 186 GLN 186 349 349 GLN GLN A . n A 1 187 MSE 187 350 350 MSE MSE A . n A 1 188 GLY 188 351 351 GLY GLY A . n A 1 189 SER 189 352 352 SER SER A . n A 1 190 GLY 190 353 353 GLY GLY A . n A 1 191 CYS 191 354 354 CYS CYS A . n A 1 192 THR 192 355 355 THR THR A . n A 1 193 ARG 193 356 356 ARG ARG A . n A 1 194 GLU 194 357 357 GLU GLU A . n A 1 195 ASN 195 358 358 ASN ASN A . n A 1 196 LEU 196 359 359 LEU LEU A . n A 1 197 GLU 197 360 360 GLU GLU A . n A 1 198 SER 198 361 361 SER SER A . n A 1 199 ILE 199 362 362 ILE ILE A . n A 1 200 ILE 200 363 363 ILE ILE A . n A 1 201 THR 201 364 364 THR THR A . n A 1 202 ASP 202 365 365 ASP ASP A . n A 1 203 PHE 203 366 366 PHE PHE A . n A 1 204 LEU 204 367 367 LEU LEU A . n A 1 205 ASN 205 368 368 ASN ASN A . n A 1 206 HIS 206 369 369 HIS HIS A . n A 1 207 LEU 207 370 370 LEU LEU A . n A 1 208 GLY 208 371 371 GLY GLY A . n A 1 209 ILE 209 372 372 ILE ILE A . n A 1 210 ASP 210 373 373 ASP ASP A . n A 1 211 PHE 211 374 374 PHE PHE A . n A 1 212 LYS 212 375 375 LYS LYS A . n A 1 213 ILE 213 376 376 ILE ILE A . n A 1 214 VAL 214 377 377 VAL VAL A . n A 1 215 GLY 215 378 378 GLY GLY A . n A 1 216 ASP 216 379 379 ASP ASP A . n A 1 217 SER 217 380 ? ? ? A . n A 1 218 CYS 218 381 ? ? ? A . n A 1 219 MSE 219 382 ? ? ? A . n A 1 220 VAL 220 383 ? ? ? A . n A 1 221 TYR 221 384 ? ? ? A . n A 1 222 GLY 222 385 385 GLY GLY A . n A 1 223 ASP 223 386 386 ASP ASP A . n A 1 224 THR 224 387 387 THR THR A . n A 1 225 LEU 225 388 388 LEU LEU A . n A 1 226 ASP 226 389 389 ASP ASP A . n A 1 227 VAL 227 390 390 VAL VAL A . n A 1 228 MSE 228 391 391 MSE MSE A . n A 1 229 HIS 229 392 392 HIS HIS A . n A 1 230 GLY 230 393 393 GLY GLY A . n A 1 231 ASP 231 394 394 ASP ASP A . n A 1 232 LEU 232 395 395 LEU LEU A . n A 1 233 GLU 233 396 396 GLU GLU A . n A 1 234 LEU 234 397 397 LEU LEU A . n A 1 235 SER 235 398 398 SER SER A . n A 1 236 SER 236 399 399 SER SER A . n A 1 237 ALA 237 400 400 ALA ALA A . n A 1 238 VAL 238 401 401 VAL VAL A . n A 1 239 VAL 239 402 402 VAL VAL A . n A 1 240 GLY 240 403 403 GLY GLY A . n A 1 241 PRO 241 404 404 PRO PRO A . n A 1 242 ILE 242 405 405 ILE ILE A . n A 1 243 PRO 243 406 406 PRO PRO A . n A 1 244 LEU 244 407 407 LEU LEU A . n A 1 245 ASP 245 408 408 ASP ASP A . n A 1 246 ARG 246 409 409 ARG ARG A . n A 1 247 GLU 247 410 410 GLU GLU A . n A 1 248 TRP 248 411 411 TRP TRP A . n A 1 249 GLY 249 412 412 GLY GLY A . n A 1 250 ILE 250 413 413 ILE ILE A . n A 1 251 ASP 251 414 414 ASP ASP A . n A 1 252 LYS 252 415 415 LYS LYS A . n A 1 253 PRO 253 416 416 PRO PRO A . n A 1 254 TRP 254 417 417 TRP TRP A . n A 1 255 ILE 255 418 418 ILE ILE A . n A 1 256 GLY 256 419 419 GLY GLY A . n A 1 257 ALA 257 420 420 ALA ALA A . n A 1 258 GLY 258 421 421 GLY GLY A . n A 1 259 PHE 259 422 422 PHE PHE A . n A 1 260 GLY 260 423 423 GLY GLY A . n A 1 261 LEU 261 424 424 LEU LEU A . n A 1 262 GLU 262 425 425 GLU GLU A . n A 1 263 ARG 263 426 426 ARG ARG A . n A 1 264 LEU 264 427 427 LEU LEU A . n A 1 265 LEU 265 428 428 LEU LEU A . n A 1 266 LYS 266 429 429 LYS LYS A . n A 1 267 VAL 267 430 430 VAL VAL A . n A 1 268 LYS 268 431 431 LYS LYS A . n A 1 269 HIS 269 432 432 HIS HIS A . n A 1 270 ASP 270 433 433 ASP ASP A . n A 1 271 PHE 271 434 434 PHE PHE A . n A 1 272 LYS 272 435 435 LYS LYS A . n A 1 273 ASN 273 436 436 ASN ASN A . n A 1 274 ILE 274 437 437 ILE ILE A . n A 1 275 LYS 275 438 438 LYS LYS A . n A 1 276 ARG 276 439 439 ARG ARG A . n A 1 277 ALA 277 440 440 ALA ALA A . n A 1 278 ALA 278 441 441 ALA ALA A . n A 1 279 ARG 279 442 442 ARG ARG A . n A 1 280 SER 280 443 443 SER SER A . n A 1 281 GLY 281 444 444 GLY GLY A . n A 1 282 SER 282 445 445 SER SER A . n A 1 283 TYR 283 446 446 TYR TYR A . n A 1 284 TYR 284 447 447 TYR TYR A . n A 1 285 ASN 285 448 448 ASN ASN A . n A 1 286 GLY 286 449 449 GLY GLY A . n A 1 287 ILE 287 450 450 ILE ILE A . n A 1 288 SER 288 451 451 SER SER A . n A 1 289 THR 289 452 452 THR THR A . n A 1 290 ASN 290 453 453 ASN ASN A . n A 1 291 LEU 291 454 454 LEU LEU A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 113 A MSE 276 ? MET SELENOMETHIONINE 2 A MSE 137 A MSE 300 ? MET SELENOMETHIONINE 3 A MSE 181 A MSE 344 ? MET SELENOMETHIONINE 4 A MSE 187 A MSE 350 ? MET SELENOMETHIONINE 5 A MSE 228 A MSE 391 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 6780 ? 1 MORE -60 ? 1 'SSA (A^2)' 23460 ? # 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' 4_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 52.5455000000 0.0000000000 -1.0000000000 0.0000000000 91.0114757091 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O2B ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OG ? A SER 236 ? A SER 399 ? 1_555 148.5 ? 2 O2B ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 O1A ? B ANP . ? A ANP 501 ? 1_555 63.3 ? 3 OG ? A SER 236 ? A SER 399 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 O1A ? B ANP . ? A ANP 501 ? 1_555 86.7 ? 4 O2B ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE1 ? A GLU 233 ? A GLU 396 ? 1_555 103.3 ? 5 OG ? A SER 236 ? A SER 399 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE1 ? A GLU 233 ? A GLU 396 ? 1_555 89.8 ? 6 O1A ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE1 ? A GLU 233 ? A GLU 396 ? 1_555 132.9 ? 7 O2B ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE2 ? A GLU 233 ? A GLU 396 ? 1_555 95.3 ? 8 OG ? A SER 236 ? A SER 399 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE2 ? A GLU 233 ? A GLU 396 ? 1_555 72.9 ? 9 O1A ? B ANP . ? A ANP 501 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE2 ? A GLU 233 ? A GLU 396 ? 1_555 87.7 ? 10 OE1 ? A GLU 233 ? A GLU 396 ? 1_555 MG ? D MG . ? A MG 503 ? 1_555 OE2 ? A GLU 233 ? A GLU 396 ? 1_555 46.9 ? 11 O1B ? B ANP . ? A ANP 501 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? E HOH . ? A HOH 734 ? 1_555 75.5 ? 12 O1B ? B ANP . ? A ANP 501 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O1G ? B ANP . ? A ANP 501 ? 1_555 66.5 ? 13 O ? E HOH . ? A HOH 734 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O1G ? B ANP . ? A ANP 501 ? 1_555 68.7 ? # 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 2013-01-02 2 'Structure model' 1 1 2013-09-04 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SOLVE phasing . ? 2 CNS refinement 1.1 ? 3 SCALEPACK 'data scaling' . ? 4 # _pdbx_entry_details.entry_id 3VQW _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;A SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSARCINA MAZEI JCM9314) DOES NOT CURRENTLY EXIST. THIS SEQUENCE CONTAINS 21 A.A. N-TERMINAL TAGS AND C-TERMINAL DOMAIN(RESIDUES 185-454) OF PYLRS. AND THIS PROTEIN IS E444G MUTANT. ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 603 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 686 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # 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 GLU A 238 ? ? -68.34 -70.71 2 1 ARG A 275 ? ? -59.88 -8.10 3 1 ASN A 280 ? ? -52.47 2.25 4 1 GLN A 287 ? ? -58.37 4.17 5 1 ASP A 292 ? ? 54.51 -162.43 6 1 ALA A 315 ? ? -149.12 -8.64 7 1 PHE A 366 ? ? -48.02 -70.43 8 1 SER A 398 ? ? -175.47 149.86 9 1 ASP A 408 ? ? -38.03 -33.25 10 1 ILE A 413 ? ? -87.70 -71.85 11 1 ASN A 453 ? ? -103.58 78.67 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MSE 164 ? A MSE 1 2 1 Y 1 A GLY 165 ? A GLY 2 3 1 Y 1 A SER 166 ? A SER 3 4 1 Y 1 A SER 167 ? A SER 4 5 1 Y 1 A HIS 168 ? A HIS 5 6 1 Y 1 A HIS 169 ? A HIS 6 7 1 Y 1 A HIS 170 ? A HIS 7 8 1 Y 1 A HIS 171 ? A HIS 8 9 1 Y 1 A HIS 172 ? A HIS 9 10 1 Y 1 A HIS 173 ? A HIS 10 11 1 Y 1 A SER 174 ? A SER 11 12 1 Y 1 A SER 175 ? A SER 12 13 1 Y 1 A GLY 176 ? A GLY 13 14 1 Y 1 A LEU 177 ? A LEU 14 15 1 Y 1 A VAL 178 ? A VAL 15 16 1 Y 1 A PRO 179 ? A PRO 16 17 1 Y 1 A ARG 180 ? A ARG 17 18 1 Y 1 A GLY 181 ? A GLY 18 19 1 Y 1 A SER 182 ? A SER 19 20 1 Y 1 A HIS 183 ? A HIS 20 21 1 Y 1 A MSE 184 ? A MSE 21 22 1 Y 1 A ALA 185 ? A ALA 22 23 1 Y 1 A SER 186 ? A SER 23 24 1 Y 1 A ALA 187 ? A ALA 24 25 1 Y 1 A ILE 208 ? A ILE 45 26 1 Y 1 A SER 209 ? A SER 46 27 1 Y 1 A LEU 210 ? A LEU 47 28 1 Y 1 A ASN 211 ? A ASN 48 29 1 Y 1 A SER 380 ? A SER 217 30 1 Y 1 A CYS 381 ? A CYS 218 31 1 Y 1 A MSE 382 ? A MSE 219 32 1 Y 1 A VAL 383 ? A VAL 220 33 1 Y 1 A TYR 384 ? A TYR 221 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' ANP 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ANP 1 501 301 ANP ANP A . C 3 MG 1 502 401 MG MG A . D 3 MG 1 503 402 MG MG A . E 4 HOH 1 601 1 HOH TIP A . E 4 HOH 2 602 2 HOH TIP A . E 4 HOH 3 603 3 HOH TIP A . E 4 HOH 4 604 4 HOH TIP A . E 4 HOH 5 605 5 HOH TIP A . E 4 HOH 6 606 6 HOH TIP A . E 4 HOH 7 607 7 HOH TIP A . E 4 HOH 8 608 8 HOH TIP A . E 4 HOH 9 609 9 HOH TIP A . E 4 HOH 10 610 10 HOH TIP A . E 4 HOH 11 611 11 HOH TIP A . E 4 HOH 12 612 12 HOH TIP A . E 4 HOH 13 613 13 HOH TIP A . E 4 HOH 14 614 14 HOH TIP A . E 4 HOH 15 615 16 HOH TIP A . E 4 HOH 16 616 17 HOH TIP A . E 4 HOH 17 617 18 HOH TIP A . E 4 HOH 18 618 19 HOH TIP A . E 4 HOH 19 619 20 HOH TIP A . E 4 HOH 20 620 21 HOH TIP A . E 4 HOH 21 621 22 HOH TIP A . E 4 HOH 22 622 23 HOH TIP A . E 4 HOH 23 623 24 HOH TIP A . E 4 HOH 24 624 25 HOH TIP A . E 4 HOH 25 625 26 HOH TIP A . E 4 HOH 26 626 27 HOH TIP A . E 4 HOH 27 627 28 HOH TIP A . E 4 HOH 28 628 29 HOH TIP A . E 4 HOH 29 629 31 HOH TIP A . E 4 HOH 30 630 33 HOH TIP A . E 4 HOH 31 631 34 HOH TIP A . E 4 HOH 32 632 35 HOH TIP A . E 4 HOH 33 633 36 HOH TIP A . E 4 HOH 34 634 38 HOH TIP A . E 4 HOH 35 635 39 HOH TIP A . E 4 HOH 36 636 40 HOH TIP A . E 4 HOH 37 637 41 HOH TIP A . E 4 HOH 38 638 42 HOH TIP A . E 4 HOH 39 639 43 HOH TIP A . E 4 HOH 40 640 44 HOH TIP A . E 4 HOH 41 641 46 HOH TIP A . E 4 HOH 42 642 48 HOH TIP A . E 4 HOH 43 643 49 HOH TIP A . E 4 HOH 44 644 50 HOH TIP A . E 4 HOH 45 645 52 HOH TIP A . E 4 HOH 46 646 54 HOH TIP A . E 4 HOH 47 647 55 HOH TIP A . E 4 HOH 48 648 56 HOH TIP A . E 4 HOH 49 649 59 HOH TIP A . E 4 HOH 50 650 60 HOH TIP A . E 4 HOH 51 651 61 HOH TIP A . E 4 HOH 52 652 62 HOH TIP A . E 4 HOH 53 653 64 HOH TIP A . E 4 HOH 54 654 65 HOH TIP A . E 4 HOH 55 655 66 HOH TIP A . E 4 HOH 56 656 67 HOH TIP A . E 4 HOH 57 657 68 HOH TIP A . E 4 HOH 58 658 69 HOH TIP A . E 4 HOH 59 659 71 HOH TIP A . E 4 HOH 60 660 72 HOH TIP A . E 4 HOH 61 661 73 HOH TIP A . E 4 HOH 62 662 76 HOH TIP A . E 4 HOH 63 663 77 HOH TIP A . E 4 HOH 64 664 78 HOH TIP A . E 4 HOH 65 665 79 HOH TIP A . E 4 HOH 66 666 80 HOH TIP A . E 4 HOH 67 667 82 HOH TIP A . E 4 HOH 68 668 84 HOH TIP A . E 4 HOH 69 669 89 HOH TIP A . E 4 HOH 70 670 91 HOH TIP A . E 4 HOH 71 671 92 HOH TIP A . E 4 HOH 72 672 94 HOH TIP A . E 4 HOH 73 673 97 HOH TIP A . E 4 HOH 74 674 100 HOH TIP A . E 4 HOH 75 675 102 HOH TIP A . E 4 HOH 76 676 103 HOH TIP A . E 4 HOH 77 677 104 HOH TIP A . E 4 HOH 78 678 105 HOH TIP A . E 4 HOH 79 679 108 HOH TIP A . E 4 HOH 80 680 109 HOH TIP A . E 4 HOH 81 681 111 HOH TIP A . E 4 HOH 82 682 113 HOH TIP A . E 4 HOH 83 683 114 HOH TIP A . E 4 HOH 84 684 115 HOH TIP A . E 4 HOH 85 685 116 HOH TIP A . E 4 HOH 86 686 118 HOH TIP A . E 4 HOH 87 687 119 HOH TIP A . E 4 HOH 88 688 120 HOH TIP A . E 4 HOH 89 689 123 HOH TIP A . E 4 HOH 90 690 124 HOH TIP A . E 4 HOH 91 691 126 HOH TIP A . E 4 HOH 92 692 127 HOH TIP A . E 4 HOH 93 693 129 HOH TIP A . E 4 HOH 94 694 131 HOH TIP A . E 4 HOH 95 695 132 HOH TIP A . E 4 HOH 96 696 133 HOH TIP A . E 4 HOH 97 697 134 HOH TIP A . E 4 HOH 98 698 135 HOH TIP A . E 4 HOH 99 699 136 HOH TIP A . E 4 HOH 100 700 137 HOH TIP A . E 4 HOH 101 701 138 HOH TIP A . E 4 HOH 102 702 139 HOH TIP A . E 4 HOH 103 703 140 HOH TIP A . E 4 HOH 104 704 141 HOH TIP A . E 4 HOH 105 705 144 HOH TIP A . E 4 HOH 106 706 146 HOH TIP A . E 4 HOH 107 707 147 HOH TIP A . E 4 HOH 108 708 148 HOH TIP A . E 4 HOH 109 709 149 HOH TIP A . E 4 HOH 110 710 151 HOH TIP A . E 4 HOH 111 711 152 HOH TIP A . E 4 HOH 112 712 153 HOH TIP A . E 4 HOH 113 713 157 HOH TIP A . E 4 HOH 114 714 158 HOH TIP A . E 4 HOH 115 715 160 HOH TIP A . E 4 HOH 116 716 161 HOH TIP A . E 4 HOH 117 717 162 HOH TIP A . E 4 HOH 118 718 164 HOH TIP A . E 4 HOH 119 719 165 HOH TIP A . E 4 HOH 120 720 167 HOH TIP A . E 4 HOH 121 721 168 HOH TIP A . E 4 HOH 122 722 170 HOH TIP A . E 4 HOH 123 723 171 HOH TIP A . E 4 HOH 124 724 172 HOH TIP A . E 4 HOH 125 725 173 HOH TIP A . E 4 HOH 126 726 174 HOH TIP A . E 4 HOH 127 727 175 HOH TIP A . E 4 HOH 128 728 176 HOH TIP A . E 4 HOH 129 729 181 HOH TIP A . E 4 HOH 130 730 182 HOH TIP A . E 4 HOH 131 731 183 HOH TIP A . E 4 HOH 132 732 185 HOH TIP A . E 4 HOH 133 733 187 HOH TIP A . E 4 HOH 134 734 188 HOH TIP A . E 4 HOH 135 735 189 HOH TIP A . E 4 HOH 136 736 190 HOH TIP A . E 4 HOH 137 737 191 HOH TIP A . E 4 HOH 138 738 193 HOH TIP A . E 4 HOH 139 739 194 HOH TIP A . E 4 HOH 140 740 195 HOH TIP A . E 4 HOH 141 741 196 HOH TIP A . E 4 HOH 142 742 197 HOH TIP A . E 4 HOH 143 743 198 HOH TIP A . #