0.036011 0.000000 0.007819 0.000000 0.017106 0.000000 0.000000 0.000000 0.030841 0.00000 0.00000 0.00000 Smith, P. Nair, P.A. Das, U. Zhu, H. Shuman, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 102.25 90.00 27.769 58.458 33.180 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mn 2 54.938 MANGANESE (II) ION non-polymer C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 S C N 76 N C N 77 N O N 78 N C N 79 N C N 80 N C N 81 N O N 82 N N N 83 N O N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 N C N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N N N 114 N C N 115 N C N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N N N 124 S C N 125 N C N 126 N O N 127 N C Y 128 N C Y 129 N N Y 130 N C Y 131 N C Y 132 N N N 133 N O N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N H N 146 N H N 147 N N N 148 S C N 149 N C N 150 N O N 151 S C N 152 N C N 153 N C N 154 N C N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N N N 170 S C N 171 N C N 172 N O N 173 N C N 174 N C N 175 N C N 176 N C N 177 N O N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N N N 192 S C N 193 N C N 194 N O N 195 N C N 196 N C N 197 N C N 198 N C N 199 N N N 200 N O N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N N N 217 S C N 218 N C N 219 N O N 220 N C N 221 N C N 222 N S N 223 N C N 224 N O N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N MN N 237 N C N 238 N O N 239 N C N 240 N O N 241 N C N 242 N C N 243 N O N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N N N 255 S C N 256 N C N 257 N O N 258 N C Y 259 N C Y 260 N C Y 261 N C Y 262 N C Y 263 N C Y 264 N C N 265 N O N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N P N 278 N O N 279 N O N 280 N O N 281 N O N 282 N N N 283 S C N 284 N C N 285 N O N 286 N C N 287 N C N 288 N C N 289 N O N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N N N 300 S C N 301 N C N 302 N O N 303 N C N 304 N O N 305 N O N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N N N 314 S C N 315 N C N 316 N O N 317 R C N 318 N O N 319 N C N 320 N O N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N N N 331 S C N 332 N C N 333 N O N 334 N C Y 335 N C Y 336 N C Y 337 N C Y 338 N N Y 339 N C Y 340 N C Y 341 N C Y 342 N C Y 343 N C N 344 N O N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N N N 358 S C N 359 N C N 360 N O N 361 N C Y 362 N C Y 363 N C Y 364 N C Y 365 N C Y 366 N C Y 367 N C N 368 N O N 369 N O N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N N N 382 S C N 383 N C N 384 N O N 385 N C N 386 N C N 387 N C N 388 N O N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing Y 127 N sing Y 128 N doub Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing Y 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N doub N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N doub N 247 N sing N 248 N sing N 249 N sing N 250 N sing Y 251 N doub Y 252 N sing Y 253 N sing N 254 N sing Y 255 N doub N 256 N sing Y 257 N doub N 258 N sing Y 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N doub N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N doub N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N doub N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N doub N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N doub N 320 N sing N 321 N sing N 322 N sing N 323 N sing Y 324 N doub Y 325 N sing Y 326 N sing N 327 N sing Y 328 N doub Y 329 N sing Y 330 N sing N 331 N sing Y 332 N sing Y 333 N doub N 334 N sing Y 335 N doub N 336 N sing Y 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N doub N 348 N sing N 349 N sing N 350 N sing N 351 N sing Y 352 N doub Y 353 N sing Y 354 N sing N 355 N sing Y 356 N doub N 357 N sing Y 358 N doub N 359 N sing Y 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N doub N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 39 3310 3320 10.1093/nar/gkq1163 21208981 Structures and activities of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily. 2011 10.2210/pdb3p4h/pdb pdb_00003p4h 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 130 1 CCD 2010-06-02 ADSC QUANTUM 315 Double silicon(111) crystal SINGLE WAVELENGTH M x-ray 1 0.95 1.0 X25 NSLS 0.95 SYNCHROTRON NSLS BEAMLINE X25 13850.097 ATP-dependent DNA ligase, N-terminal domain protein 1 man polymer 54.938 MANGANESE (II) ION 1 syn non-polymer 94.971 PHOSPHATE ION 1 syn non-polymer 106.120 DI(HYDROXYETHYL)ETHER 1 syn non-polymer 18.015 water 216 nat water no no SMPRFVVQEHHARRLHWDLRLEMDNVLKSWALPKGVPEKRGVKRLAIETEDHDLSYIDFEGRIPEGMYGAGEVKIWDSGE YELLERTENKIKFLAKGRKMNGEYVLIKTKVGWLLMKA SMPRFVVQEHHARRLHWDLRLEMDNVLKSWALPKGVPEKRGVKRLAIETEDHDLSYIDFEGRIPEGMYGAGEVKIWDSGE YELLERTENKIKFLAKGRKMNGEYVLIKTKVGWLLMKA A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n OPF8 sample Kcr_0736 374847 Candidatus Korarchaeum cryptofilum 469008 Escherichia coli BL21(DE3)RIL PLASMID pET28bSmt3His10 1 1.90 35.27 VAPOR DIFFUSION, SITTING DROP 9.5 Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 1.8 mM MnCl2 and reservoir solution containing 20% PEG 3350 and 0.2 M Na2HPO4 , pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Source and taxonomy Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2011-01-19 1 1 2011-07-13 1 2 2023-09-06 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2010-10-06 REL REL MN MANGANESE (II) ION PO4 PHOSPHATE ION PEG DI(HYDROXYETHYL)ETHER HOH water 3N9B PDB ENTRY 3N9B PDB experimental model MN 1 2 MN MN 118 A PO4 2 3 PO4 PO4 119 A PEG 3 4 PEG PEG 120 A HOH 121 5 HOH HOH 121 A HOH 122 5 HOH HOH 122 A HOH 123 5 HOH HOH 123 A HOH 124 5 HOH HOH 124 A HOH 125 5 HOH HOH 125 A HOH 126 5 HOH HOH 126 A HOH 127 5 HOH HOH 127 A HOH 128 5 HOH HOH 128 A HOH 129 5 HOH HOH 129 A HOH 130 5 HOH HOH 130 A HOH 131 5 HOH HOH 131 A HOH 132 5 HOH HOH 132 A HOH 133 5 HOH HOH 133 A HOH 134 5 HOH HOH 134 A HOH 135 5 HOH HOH 135 A HOH 136 5 HOH HOH 136 A HOH 137 5 HOH HOH 137 A HOH 138 5 HOH HOH 138 A HOH 139 5 HOH HOH 139 A HOH 140 5 HOH HOH 140 A HOH 141 5 HOH HOH 141 A HOH 142 5 HOH HOH 142 A HOH 143 5 HOH HOH 143 A HOH 144 5 HOH HOH 144 A HOH 145 5 HOH HOH 145 A HOH 146 5 HOH HOH 146 A HOH 147 5 HOH HOH 147 A HOH 148 5 HOH HOH 148 A HOH 149 5 HOH HOH 149 A HOH 150 5 HOH HOH 150 A HOH 151 5 HOH HOH 151 A HOH 152 5 HOH HOH 152 A HOH 153 5 HOH HOH 153 A HOH 154 5 HOH HOH 154 A HOH 155 5 HOH HOH 155 A HOH 156 5 HOH HOH 156 A HOH 157 5 HOH HOH 157 A HOH 158 5 HOH HOH 158 A HOH 159 5 HOH HOH 159 A HOH 160 5 HOH HOH 160 A HOH 161 5 HOH HOH 161 A HOH 162 5 HOH HOH 162 A HOH 163 5 HOH HOH 163 A HOH 164 5 HOH HOH 164 A HOH 165 5 HOH HOH 165 A HOH 166 5 HOH HOH 166 A HOH 167 5 HOH HOH 167 A HOH 168 5 HOH HOH 168 A HOH 169 5 HOH HOH 169 A HOH 170 5 HOH HOH 170 A HOH 171 5 HOH HOH 171 A HOH 172 5 HOH HOH 172 A HOH 173 5 HOH HOH 173 A HOH 174 5 HOH HOH 174 A HOH 175 5 HOH HOH 175 A HOH 176 5 HOH HOH 176 A HOH 177 5 HOH HOH 177 A HOH 178 5 HOH HOH 178 A HOH 179 5 HOH HOH 179 A HOH 180 5 HOH HOH 180 A HOH 181 5 HOH HOH 181 A HOH 182 5 HOH HOH 182 A HOH 183 5 HOH HOH 183 A HOH 184 5 HOH HOH 184 A HOH 185 5 HOH HOH 185 A HOH 186 5 HOH HOH 186 A HOH 187 5 HOH HOH 187 A HOH 188 5 HOH HOH 188 A HOH 189 5 HOH HOH 189 A HOH 190 5 HOH HOH 190 A HOH 191 5 HOH HOH 191 A HOH 192 5 HOH HOH 192 A HOH 193 5 HOH HOH 193 A HOH 194 5 HOH HOH 194 A HOH 195 5 HOH HOH 195 A HOH 196 5 HOH HOH 196 A HOH 197 5 HOH HOH 197 A HOH 198 5 HOH HOH 198 A HOH 199 5 HOH HOH 199 A HOH 200 5 HOH HOH 200 A HOH 201 5 HOH HOH 201 A HOH 202 5 HOH HOH 202 A HOH 203 5 HOH HOH 203 A HOH 204 5 HOH HOH 204 A HOH 205 5 HOH HOH 205 A HOH 206 5 HOH HOH 206 A HOH 207 5 HOH HOH 207 A HOH 208 5 HOH HOH 208 A HOH 209 5 HOH HOH 209 A HOH 210 5 HOH HOH 210 A HOH 211 5 HOH HOH 211 A HOH 212 5 HOH HOH 212 A HOH 213 5 HOH HOH 213 A HOH 214 5 HOH HOH 214 A HOH 215 5 HOH HOH 215 A HOH 39 5 HOH HOH 216 A HOH 1 5 HOH HOH 217 A HOH 2 5 HOH HOH 218 A HOH 3 5 HOH HOH 219 A HOH 4 5 HOH HOH 220 A HOH 5 5 HOH HOH 221 A HOH 6 5 HOH HOH 222 A HOH 7 5 HOH HOH 223 A HOH 8 5 HOH HOH 224 A HOH 9 5 HOH HOH 225 A HOH 10 5 HOH HOH 226 A HOH 11 5 HOH HOH 227 A HOH 12 5 HOH HOH 228 A HOH 13 5 HOH HOH 229 A HOH 14 5 HOH HOH 230 A HOH 15 5 HOH HOH 231 A HOH 16 5 HOH HOH 232 A HOH 17 5 HOH HOH 233 A HOH 18 5 HOH HOH 234 A HOH 19 5 HOH HOH 235 A HOH 20 5 HOH HOH 236 A HOH 21 5 HOH HOH 237 A HOH 22 5 HOH HOH 238 A HOH 23 5 HOH HOH 239 A HOH 24 5 HOH HOH 240 A HOH 25 5 HOH HOH 241 A HOH 26 5 HOH HOH 242 A HOH 27 5 HOH HOH 243 A HOH 28 5 HOH HOH 244 A HOH 29 5 HOH HOH 245 A HOH 30 5 HOH HOH 246 A HOH 31 5 HOH HOH 247 A HOH 32 5 HOH HOH 248 A HOH 33 5 HOH HOH 249 A HOH 34 5 HOH HOH 250 A HOH 35 5 HOH HOH 251 A HOH 36 5 HOH HOH 252 A HOH 37 5 HOH HOH 253 A HOH 38 5 HOH HOH 254 A HOH 39 5 HOH HOH 255 A HOH 40 5 HOH HOH 256 A HOH 41 5 HOH HOH 257 A HOH 42 5 HOH HOH 258 A HOH 43 5 HOH HOH 259 A HOH 44 5 HOH HOH 260 A HOH 45 5 HOH HOH 261 A HOH 46 5 HOH HOH 262 A HOH 47 5 HOH HOH 263 A HOH 48 5 HOH HOH 264 A HOH 49 5 HOH HOH 265 A HOH 50 5 HOH HOH 266 A HOH 51 5 HOH HOH 267 A HOH 52 5 HOH HOH 268 A HOH 53 5 HOH HOH 269 A HOH 54 5 HOH HOH 270 A HOH 55 5 HOH HOH 271 A HOH 56 5 HOH HOH 272 A HOH 57 5 HOH HOH 273 A HOH 58 5 HOH HOH 274 A HOH 59 5 HOH HOH 275 A HOH 60 5 HOH HOH 276 A HOH 61 5 HOH HOH 277 A HOH 62 5 HOH HOH 278 A HOH 63 5 HOH HOH 279 A HOH 64 5 HOH HOH 280 A HOH 65 5 HOH HOH 281 A HOH 66 5 HOH HOH 282 A HOH 67 5 HOH HOH 283 A HOH 68 5 HOH HOH 284 A HOH 69 5 HOH HOH 285 A HOH 70 5 HOH HOH 286 A HOH 71 5 HOH HOH 287 A HOH 72 5 HOH HOH 288 A HOH 73 5 HOH HOH 289 A HOH 74 5 HOH HOH 290 A HOH 75 5 HOH HOH 291 A HOH 76 5 HOH HOH 292 A HOH 77 5 HOH HOH 293 A HOH 78 5 HOH HOH 294 A HOH 79 5 HOH HOH 295 A HOH 80 5 HOH HOH 296 A HOH 81 5 HOH HOH 297 A HOH 82 5 HOH HOH 298 A HOH 83 5 HOH HOH 299 A HOH 84 5 HOH HOH 300 A HOH 85 5 HOH HOH 301 A HOH 86 5 HOH HOH 302 A HOH 87 5 HOH HOH 303 A HOH 88 5 HOH HOH 304 A HOH 89 5 HOH HOH 305 A HOH 90 5 HOH HOH 306 A HOH 91 5 HOH HOH 307 A HOH 92 5 HOH HOH 308 A HOH 93 5 HOH HOH 309 A HOH 94 5 HOH HOH 310 A HOH 95 5 HOH HOH 311 A HOH 96 5 HOH HOH 312 A HOH 97 5 HOH HOH 313 A HOH 98 5 HOH HOH 314 A HOH 99 5 HOH HOH 315 A HOH 100 5 HOH HOH 316 A HOH 101 5 HOH HOH 317 A HOH 102 5 HOH HOH 318 A HOH 103 5 HOH HOH 319 A HOH 104 5 HOH HOH 320 A HOH 105 5 HOH HOH 321 A HOH 106 5 HOH HOH 322 A HOH 107 5 HOH HOH 323 A HOH 108 5 HOH HOH 324 A HOH 109 5 HOH HOH 325 A HOH 110 5 HOH HOH 326 A HOH 111 5 HOH HOH 327 A HOH 112 5 HOH HOH 328 A HOH 113 5 HOH HOH 329 A HOH 114 5 HOH HOH 330 A HOH 115 5 HOH HOH 331 A HOH 116 5 HOH HOH 332 A HOH 117 5 HOH HOH 333 A HOH 118 5 HOH HOH 334 A HOH 119 5 HOH HOH 335 A HOH 120 5 HOH HOH 336 A SER 0 n 1 SER 0 A MET 1 n 2 MET 1 A PRO 2 n 3 PRO 2 A ARG 3 n 4 ARG 3 A PHE 4 n 5 PHE 4 A VAL 5 n 6 VAL 5 A VAL 6 n 7 VAL 6 A GLN 7 n 8 GLN 7 A GLU 8 n 9 GLU 8 A HIS 9 n 10 HIS 9 A HIS 10 n 11 HIS 10 A ALA 11 n 12 ALA 11 A ARG 12 n 13 ARG 12 A ARG 13 n 14 ARG 13 A LEU 14 n 15 LEU 14 A HIS 15 n 16 HIS 15 A TRP 16 n 17 TRP 16 A ASP 17 n 18 ASP 17 A LEU 18 n 19 LEU 18 A ARG 19 n 20 ARG 19 A LEU 20 n 21 LEU 20 A GLU 21 n 22 GLU 21 A MET 22 n 23 MET 22 A ASP 23 n 24 ASP 23 A ASN 24 n 25 ASN 24 A VAL 25 n 26 VAL 25 A LEU 26 n 27 LEU 26 A LYS 27 n 28 LYS 27 A SER 28 n 29 SER 28 A TRP 29 n 30 TRP 29 A ALA 30 n 31 ALA 30 A LEU 31 n 32 LEU 31 A PRO 32 n 33 PRO 32 A LYS 33 n 34 LYS 33 A GLY 34 n 35 GLY 34 A VAL 35 n 36 VAL 35 A PRO 36 n 37 PRO 36 A GLU 37 n 38 GLU 37 A LYS 38 n 39 LYS 38 A ARG 39 n 40 ARG 39 A GLY 40 n 41 GLY 40 A VAL 41 n 42 VAL 41 A LYS 42 n 43 LYS 42 A ARG 43 n 44 ARG 43 A LEU 44 n 45 LEU 44 A ALA 45 n 46 ALA 45 A ILE 46 n 47 ILE 46 A GLU 47 n 48 GLU 47 A THR 48 n 49 THR 48 A GLU 49 n 50 GLU 49 A ASP 50 n 51 ASP 50 A HIS 51 n 52 HIS 51 A ASP 52 n 53 ASP 52 A LEU 53 n 54 LEU 53 A SER 54 n 55 SER 54 A TYR 55 n 56 TYR 55 A ILE 56 n 57 ILE 56 A ASP 57 n 58 ASP 57 A PHE 58 n 59 PHE 58 A GLU 59 n 60 GLU 59 A GLY 60 n 61 GLY 60 A ARG 61 n 62 ARG 61 A ILE 62 n 63 ILE 62 A PRO 63 n 64 PRO 63 A GLU 64 n 65 GLU 64 A GLY 65 n 66 GLY 65 A MET 66 n 67 MET 66 A TYR 67 n 68 TYR 67 A GLY 68 n 69 GLY 68 A ALA 69 n 70 ALA 69 A GLY 70 n 71 GLY 70 A GLU 71 n 72 GLU 71 A VAL 72 n 73 VAL 72 A LYS 73 n 74 LYS 73 A ILE 74 n 75 ILE 74 A TRP 75 n 76 TRP 75 A ASP 76 n 77 ASP 76 A SER 77 n 78 SER 77 A GLY 78 n 79 GLY 78 A GLU 79 n 80 GLU 79 A TYR 80 n 81 TYR 80 A GLU 81 n 82 GLU 81 A LEU 82 n 83 LEU 82 A LEU 83 n 84 LEU 83 A GLU 84 n 85 GLU 84 A ARG 85 n 86 ARG 85 A THR 86 n 87 THR 86 A GLU 87 n 88 GLU 87 A ASN 88 n 89 ASN 88 A LYS 89 n 90 LYS 89 A ILE 90 n 91 ILE 90 A LYS 91 n 92 LYS 91 A PHE 92 n 93 PHE 92 A LEU 93 n 94 LEU 93 A ALA 94 n 95 ALA 94 A LYS 95 n 96 LYS 95 A GLY 96 n 97 GLY 96 A ARG 97 n 98 ARG 97 A LYS 98 n 99 LYS 98 A MET 99 n 100 MET 99 A ASN 100 n 101 ASN 100 A GLY 101 n 102 GLY 101 A GLU 102 n 103 GLU 102 A TYR 103 n 104 TYR 103 A VAL 104 n 105 VAL 104 A LEU 105 n 106 LEU 105 A ILE 106 n 107 ILE 106 A LYS 107 n 108 LYS 107 A THR 108 n 109 THR 108 A LYS 109 n 110 LYS 109 A VAL 110 n 111 VAL 110 A GLY 111 n 112 GLY 111 A TRP 112 n 113 TRP 112 A LEU 113 n 114 LEU 113 A LEU 114 n 115 LEU 114 A MET 115 n 116 MET 115 A LYS 116 n 117 LYS 116 A ALA 117 n 118 ALA 117 A author_and_software_defined_assembly PISA 1 monomeric A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 A HIS 15 A NE2 HIS 16 1_555 88.2 A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 A ASP 17 A OD2 ASP 18 1_555 97.8 A HIS 15 A NE2 HIS 16 1_555 A MN 118 B MN MN 1_555 A ASP 17 A OD2 ASP 18 1_555 92.9 A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 A PO4 119 C O4 PO4 1_555 98.0 A HIS 15 A NE2 HIS 16 1_555 A MN 118 B MN MN 1_555 A PO4 119 C O4 PO4 1_555 171.4 A ASP 17 A OD2 ASP 18 1_555 A MN 118 B MN MN 1_555 A PO4 119 C O4 PO4 1_555 92.1 A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 A HOH 247 E O HOH 1_555 166.4 A HIS 15 A NE2 HIS 16 1_555 A MN 118 B MN MN 1_555 A HOH 247 E O HOH 1_555 85.4 A ASP 17 A OD2 ASP 18 1_555 A MN 118 B MN MN 1_555 A HOH 247 E O HOH 1_555 94.5 A PO4 119 C O4 PO4 1_555 A MN 118 B MN MN 1_555 A HOH 247 E O HOH 1_555 87.2 A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 86.7 A HIS 15 A NE2 HIS 16 1_555 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 89.9 A ASP 17 A OD2 ASP 18 1_555 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 174.7 A PO4 119 C O4 PO4 1_555 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 84.6 A HOH 247 E O HOH 1_555 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 81.3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N GLY 60 A N GLY 61 A O VAL 72 A O VAL 73 A N LEU 83 A N LEU 84 A O LYS 91 A O LYS 92 A N PHE 92 A N PHE 93 A O TYR 103 A O TYR 104 A N THR 108 A N THR 109 A O GLY 111 A O GLY 112 A O LEU 114 A O LEU 115 A N ARG 43 A N ARG 44 A O ILE 46 A O ILE 47 A N ALA 30 A N ALA 31 A O LEU 31 A O LEU 32 A N TRP 16 A N TRP 17 A O HIS 15 A O HIS 16 A N HIS 9 A N HIS 10 A N VAL 6 A N VAL 7 A O ASP 76 A O ASP 77 1 A N SER 0 A N SER 1 1 Y 1 A CB SER 0 A CB SER 1 1 Y 1 A OG SER 0 A OG SER 1 1 Y 1 A CD LYS 38 A CD LYS 39 1 Y 1 A CE LYS 38 A CE LYS 39 1 Y 1 A NZ LYS 38 A NZ LYS 39 1 Y 1 A CD ARG 97 A CD ARG 98 1 Y 1 A NE ARG 97 A NE ARG 98 1 Y 1 A CZ ARG 97 A CZ ARG 98 1 Y 1 A NH1 ARG 97 A NH1 ARG 98 1 Y 1 A NH2 ARG 97 A NH2 ARG 98 1 Y 1 A A OH O TYR HOH 103 281 1.98 B 1 A A OD2 O ASP HOH 57 187 2.05 B 1 A A OD2 O ASP HOH 57 214 2.19 B 1 A A O O MET HOH 66 207 2.19 1 A A O O HOH HOH 137 174 2.04 1_555 1_655 1 A A O O HOH HOH 272 314 2.16 1_555 1_556 1 A ALA 11 -102.23 -164.98 1 A ALA 69 B -48.93 150.45 1.2895 -0.0000 1.2613 -1.9815 -0.0000 0.4927 0.1647 0.1321 0.1354 1.100 23.397 4161 42013 40516 10.27 96.49 0.10 Random 1 1.34 MOLECULAR REPLACEMENT 16.11 0.77 0.90 PDB ENTRY 3N9B ML FLAT BULK SOLVENT MODEL 37.996 0.293 1.100 23.397 216 1192 13 0 963 0.011 1213 1.406 1659 13.155 501 0.095 166 0.007 218 0.2064 0.1883 1.1393 401 3439 3439 92.00 0.1980 0.1572 1.1849 385 3479 3479 92.00 0.2140 0.1599 1.2389 390 3512 3512 93.00 0.1978 0.1516 1.3042 401 3567 3567 95.00 0.1839 0.1295 1.3859 429 3637 3637 97.00 0.1702 0.1223 1.4929 436 3659 3659 98.00 0.1525 0.1112 1.6430 439 3719 3719 99.00 0.1621 0.1180 1.8807 433 3737 3737 99.00 0.1601 0.1238 2.3691 423 3772 3772 100.00 0.1522 0.1343 23.4026 424 3834 3834 100.00 10.9 1.1 30.0 3P4H 42013 40543 -3.0 0.038 1 42.0 5.1 96.5 0.372 1.1 1.12 2.07 1 2.3 90.8 data collection HKL-2000 phasing SOLVE refinement PHENIX (phenix.refine: 1.6.4_486) data reduction HKL-2000 data scaling SCALEPACK Structures of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily 1 N N 2 N N 3 N N 4 N N 5 N N A ASP 52 A ASP 53 HELX_P A PHE 58 A PHE 59 5 1 7 metalc 2.334 A HIS 9 A ND1 HIS 10 1_555 A MN 118 B MN MN 1_555 metalc 2.226 A HIS 15 A NE2 HIS 16 1_555 A MN 118 B MN MN 1_555 metalc 2.163 A ASP 17 A OD2 ASP 18 1_555 A MN 118 B MN MN 1_555 metalc 2.187 A MN 118 B MN MN 1_555 A PO4 119 C O4 PO4 1_555 metalc 2.294 A MN 118 B MN MN 1_555 A HOH 247 E O HOH 1_555 metalc 2.318 A MN 118 B MN MN 1_555 A HOH 249 E O HOH 1_555 HYDROLASE Phosphoesterase, Metalloenzyme, Manganese, beta barrel, phosphatase, HYDROLASE B1L4V6_KORCO UNP 1 1 B1L4V6 MPRFVVQEHHARRLHWDLRLEMDNVLKSWALPKGVPEKRGVKRLAIETEDHDLSYIDFEGRIPEGMYGAGEVKIWDSGEY ELLERTENKIKFLAKGRKMNGEYVLIKTKVGWLLMKA 1 117 3P4H 1 117 B1L4V6 A 1 2 118 1 expression tag SER 0 3P4H A B1L4V6 UNP 1 10 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A GLY 60 A GLY 61 A ILE 62 A ILE 63 A GLY 70 A GLY 71 A THR 86 A THR 87 A LYS 89 A LYS 90 A LYS 95 A LYS 96 A ASN 100 A ASN 101 A THR 108 A THR 109 A GLY 111 A GLY 112 A LYS 116 A LYS 117 A LYS 42 A LYS 43 A HIS 51 A HIS 52 A VAL 25 A VAL 26 A LEU 31 A LEU 32 A LEU 14 A LEU 15 A MET 22 A MET 23 A ARG 3 A ARG 4 A HIS 10 A HIS 11 A GLY 70 A GLY 71 A THR 86 A THR 87 BINDING SITE FOR RESIDUE MN A 118 A MN 118 Software 6 BINDING SITE FOR RESIDUE PO4 A 119 A PO4 119 Software 12 BINDING SITE FOR RESIDUE PEG A 120 A PEG 120 Software 13 A HIS 9 A HIS 10 6 1_555 A HIS 15 A HIS 16 6 1_555 A ASP 17 A ASP 18 6 1_555 A PO4 119 C PO4 6 1_555 A HOH 247 E HOH 6 1_555 A HOH 249 E HOH 6 1_555 A HIS 9 A HIS 10 12 1_555 A ASP 17 A ASP 18 12 1_555 A ARG 19 A ARG 20 12 1_555 A HIS 51 A HIS 52 12 1_555 A GLY 68 A GLY 69 12 1_555 A MN 118 B MN 12 1_555 A PEG 120 D PEG 12 1_455 A HOH 227 E HOH 12 1_555 A HOH 247 E HOH 12 1_555 A HOH 249 E HOH 12 1_555 A HOH 250 E HOH 12 1_555 A HOH 310 E HOH 12 1_555 A HIS 15 A HIS 16 13 1_655 A ALA 30 A ALA 31 13 1_655 A THR 48 A THR 49 13 1_655 A GLU 49 A GLU 50 13 1_655 A ARG 97 A ARG 98 13 1_555 A PO4 119 C PO4 13 1_655 A HOH 145 E HOH 13 1_555 A HOH 192 E HOH 13 1_655 A HOH 200 E HOH 13 1_655 A HOH 247 E HOH 13 1_655 A HOH 312 E HOH 13 1_555 A HOH 315 E HOH 13 1_555 A HOH 315 E HOH 13 1_655 4 P 1 21 1