0.008679 0.000000 0.000000 0.000000 0.007533 0.000000 0.000000 0.000000 0.016857 0.00000 0.00000 0.00000 Lee, J.H. Na, Y. Eom, S.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 115.216 132.744 59.324 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 C3 H7 N O2 S 121.158 y CYSTEINE 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 C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking 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 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O 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 H N 124 N H N 125 N H N 126 N H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C N 169 N O N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N N N 184 S C N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N C N 213 N N N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C N 235 N C N 236 N S N 237 N C N 238 N O N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H 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 N N 251 S C N 252 N C N 253 N O N 254 N C Y 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C N 261 N O N 262 N H N 263 N H N 264 N H N 265 N H 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 N N 274 S C N 275 N C N 276 N O N 277 N C N 278 N C N 279 N C N 280 N O N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N O N 296 N O N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N N N 305 S C N 306 N C N 307 N O N 308 R C N 309 N O N 310 N C N 311 N O N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N N N 322 S C N 323 N C N 324 N O N 325 N C Y 326 N C Y 327 N C Y 328 N C Y 329 N N Y 330 N C Y 331 N C Y 332 N C Y 333 N C Y 334 N C N 335 N O N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N N N 349 S C N 350 N C N 351 N O N 352 N C Y 353 N C Y 354 N C Y 355 N C Y 356 N C Y 357 N C Y 358 N C N 359 N O N 360 N O N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N N N 373 S C N 374 N C N 375 N O N 376 N C N 377 N C N 378 N C N 379 N O N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 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 sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N doub N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 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 doub 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 sing 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 doub 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 sing 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 doub 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 sing 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 doub 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 doub N 244 N sing N 245 N sing N 246 N sing N 247 N sing Y 248 N doub Y 249 N sing Y 250 N sing N 251 N sing Y 252 N doub N 253 N sing Y 254 N doub N 255 N sing Y 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N doub 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 sing 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 doub 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 sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N doub 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 sing 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 doub N 313 N sing N 314 N sing N 315 N sing N 316 N sing Y 317 N doub Y 318 N sing Y 319 N sing N 320 N sing Y 321 N doub Y 322 N sing Y 323 N sing N 324 N sing Y 325 N sing Y 326 N doub N 327 N sing Y 328 N doub N 329 N sing Y 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N doub N 341 N sing N 342 N sing N 343 N sing N 344 N sing Y 345 N doub Y 346 N sing Y 347 N sing N 348 N sing Y 349 N doub N 350 N sing Y 351 N doub N 352 N sing Y 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N doub 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 sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing US Proteins PSFGEY 0867 0887-3585 64 1078 1082 10.1002/prot.20927 16779845 Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes 2006 10.2210/pdb2fb9/pdb pdb_00002fb9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 CCD 2004-11-24 ADSC QUANTUM 4 GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.0 1.0 BL-6B Photon Factory 1.0 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 35107.293 D-alanine:D-alanine ligase 6.3.2.4 1 man polymer 18.015 water 115 nat water no no MEFMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVV FPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANT GSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELL IPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELA LT MEFMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVV FPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANT GSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELL IPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELA LT 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 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 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 Thermus Escherichia sample 272 Thermus caldophilus 562 Escherichia coli plasmid pKK223-3 1 3.23 61.89 VAPOR DIFFUSION, HANGING DROP 8.5 29%(w/v) PEG MME 2000, 0.1M Tris-HCl, 0.2M Sodium Acetate, 0.2M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K 294 chem_comp_atom chem_comp_bond database_2 struct_ref_seq_dif repository Initial release Version format compliance Derived calculations Version format compliance Data collection Database references 1 0 2006-08-29 1 1 2008-05-01 1 2 2011-07-13 1 3 2024-03-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details RCSB Y PDBJ 2005-12-08 REL REL HOH water TIP 1 2 HOH HOH 323 A TIP 2 2 HOH HOH 324 A TIP 3 2 HOH HOH 325 A TIP 4 2 HOH HOH 326 A TIP 5 2 HOH HOH 327 A TIP 6 2 HOH HOH 328 A TIP 7 2 HOH HOH 329 A TIP 8 2 HOH HOH 330 A TIP 9 2 HOH HOH 331 A TIP 10 2 HOH HOH 332 A TIP 11 2 HOH HOH 333 A TIP 12 2 HOH HOH 334 A TIP 13 2 HOH HOH 335 A TIP 14 2 HOH HOH 336 A TIP 15 2 HOH HOH 337 A TIP 16 2 HOH HOH 338 A TIP 17 2 HOH HOH 339 A TIP 18 2 HOH HOH 340 A TIP 19 2 HOH HOH 341 A TIP 20 2 HOH HOH 342 A TIP 21 2 HOH HOH 343 A TIP 22 2 HOH HOH 344 A TIP 23 2 HOH HOH 345 A TIP 24 2 HOH HOH 346 A TIP 25 2 HOH HOH 347 A TIP 26 2 HOH HOH 348 A TIP 27 2 HOH HOH 349 A TIP 28 2 HOH HOH 350 A TIP 29 2 HOH HOH 351 A TIP 30 2 HOH HOH 352 A TIP 31 2 HOH HOH 353 A TIP 32 2 HOH HOH 354 A TIP 33 2 HOH HOH 355 A TIP 34 2 HOH HOH 356 A TIP 35 2 HOH HOH 357 A TIP 36 2 HOH HOH 358 A TIP 37 2 HOH HOH 359 A TIP 38 2 HOH HOH 360 A TIP 39 2 HOH HOH 361 A TIP 40 2 HOH HOH 362 A TIP 41 2 HOH HOH 363 A TIP 42 2 HOH HOH 364 A TIP 43 2 HOH HOH 365 A TIP 44 2 HOH HOH 366 A TIP 45 2 HOH HOH 367 A TIP 46 2 HOH HOH 368 A TIP 47 2 HOH HOH 369 A TIP 48 2 HOH HOH 370 A TIP 49 2 HOH HOH 371 A TIP 50 2 HOH HOH 372 A TIP 51 2 HOH HOH 373 A TIP 52 2 HOH HOH 374 A TIP 53 2 HOH HOH 375 A TIP 54 2 HOH HOH 376 A TIP 55 2 HOH HOH 377 A TIP 56 2 HOH HOH 378 A TIP 57 2 HOH HOH 379 A TIP 58 2 HOH HOH 380 A TIP 59 2 HOH HOH 381 A TIP 60 2 HOH HOH 382 A TIP 61 2 HOH HOH 383 A TIP 62 2 HOH HOH 384 A TIP 63 2 HOH HOH 385 A TIP 64 2 HOH HOH 386 A TIP 65 2 HOH HOH 387 A TIP 66 2 HOH HOH 388 A TIP 67 2 HOH HOH 389 A TIP 68 2 HOH HOH 390 A TIP 69 2 HOH HOH 391 A TIP 70 2 HOH HOH 392 A TIP 71 2 HOH HOH 393 A TIP 72 2 HOH HOH 394 A TIP 73 2 HOH HOH 395 A TIP 74 2 HOH HOH 396 A TIP 75 2 HOH HOH 397 A TIP 76 2 HOH HOH 398 A TIP 77 2 HOH HOH 399 A TIP 78 2 HOH HOH 400 A TIP 79 2 HOH HOH 401 A TIP 80 2 HOH HOH 402 A TIP 81 2 HOH HOH 403 A TIP 82 2 HOH HOH 404 A TIP 83 2 HOH HOH 405 A TIP 84 2 HOH HOH 406 A TIP 85 2 HOH HOH 407 A TIP 86 2 HOH HOH 408 A TIP 87 2 HOH HOH 409 A TIP 88 2 HOH HOH 410 A TIP 89 2 HOH HOH 411 A TIP 90 2 HOH HOH 412 A TIP 91 2 HOH HOH 413 A TIP 92 2 HOH HOH 414 A TIP 93 2 HOH HOH 415 A TIP 94 2 HOH HOH 416 A TIP 95 2 HOH HOH 417 A TIP 96 2 HOH HOH 418 A TIP 97 2 HOH HOH 419 A TIP 98 2 HOH HOH 420 A TIP 99 2 HOH HOH 421 A TIP 100 2 HOH HOH 422 A TIP 101 2 HOH HOH 423 A TIP 102 2 HOH HOH 424 A TIP 103 2 HOH HOH 425 A TIP 104 2 HOH HOH 426 A TIP 105 2 HOH HOH 427 A TIP 106 2 HOH HOH 428 A TIP 107 2 HOH HOH 429 A TIP 108 2 HOH HOH 430 A TIP 109 2 HOH HOH 431 A TIP 110 2 HOH HOH 432 A TIP 111 2 HOH HOH 433 A TIP 112 2 HOH HOH 434 A TIP 113 2 HOH HOH 435 A TIP 114 2 HOH HOH 436 A TIP 115 2 HOH HOH 437 A MET 1 n 1 MET 1 A GLU 2 n 2 GLU 2 A PHE 3 n 3 PHE 3 A MET 4 n 4 MET 4 A ARG 5 n 5 ARG 5 A VAL 6 n 6 VAL 6 A LEU 7 n 7 LEU 7 A LEU 8 n 8 LEU 8 A ILE 9 n 9 ILE 9 A ALA 10 n 10 ALA 10 A GLY 11 n 11 GLY 11 A GLY 12 n 12 GLY 12 A VAL 13 n 13 VAL 13 A SER 14 n 14 SER 14 A PRO 15 n 15 PRO 15 A GLU 16 n 16 GLU 16 A HIS 17 n 17 HIS 17 A GLU 18 n 18 GLU 18 A VAL 19 n 19 VAL 19 A SER 20 n 20 SER 20 A LEU 21 n 21 LEU 21 A LEU 22 n 22 LEU 22 A SER 23 n 23 SER 23 A ALA 24 n 24 ALA 24 A GLU 25 n 25 GLU 25 A GLY 26 n 26 GLY 26 A VAL 27 n 27 VAL 27 A LEU 28 n 28 LEU 28 A ARG 29 n 29 ARG 29 A HIS 30 n 30 HIS 30 A ILE 31 n 31 ILE 31 A PRO 32 n 32 PRO 32 A PHE 33 n 33 PHE 33 A PRO 34 n 34 PRO 34 A THR 35 n 35 THR 35 A ASP 36 n 36 ASP 36 A LEU 37 n 37 LEU 37 A ALA 38 n 38 ALA 38 A VAL 39 n 39 VAL 39 A ILE 40 n 40 ILE 40 A ALA 41 n 41 ALA 41 A GLN 42 n 42 GLN 42 A ASP 43 n 43 ASP 43 A GLY 44 n 44 GLY 44 A ARG 45 n 45 ARG 45 A TRP 46 n 46 TRP 46 A LEU 47 n 47 LEU 47 A LEU 48 n 48 LEU 48 A GLY 49 n 49 GLY 49 A GLU 50 n 50 GLU 50 A LYS 51 n 51 LYS 51 A ALA 52 n 52 ALA 52 A LEU 53 n 53 LEU 53 A THR 54 n 54 THR 54 A ALA 55 n 55 ALA 55 A LEU 56 n 56 LEU 56 A GLU 57 n 57 GLU 57 A ALA 58 n 58 ALA 58 A LYS 59 n 59 LYS 59 A ALA 60 n 60 ALA 60 A ALA 61 n 61 ALA 61 A PRO 62 n 62 PRO 62 A GLU 63 n 63 GLU 63 A GLY 64 n 64 GLY 64 A GLU 65 n 65 GLU 65 A HIS 66 n 66 HIS 66 A PRO 67 n 67 PRO 67 A PHE 68 n 68 PHE 68 A PRO 69 n 69 PRO 69 A PRO 70 n 70 PRO 70 A PRO 71 n 71 PRO 71 A LEU 72 n 72 LEU 72 A SER 73 n 73 SER 73 A TRP 74 n 74 TRP 74 A GLU 75 n 75 GLU 75 A ARG 76 n 76 ARG 76 A TYR 77 n 77 TYR 77 A ASP 78 n 78 ASP 78 A VAL 79 n 79 VAL 79 A VAL 80 n 80 VAL 80 A PHE 81 n 81 PHE 81 A PRO 82 n 82 PRO 82 A LEU 83 n 83 LEU 83 A LEU 84 n 84 LEU 84 A HIS 85 n 85 HIS 85 A GLY 86 n 86 GLY 86 A ARG 87 n 87 ARG 87 A PHE 88 n 88 PHE 88 A GLY 89 n 89 GLY 89 A GLU 90 n 90 GLU 90 A ASP 91 n 91 ASP 91 A GLY 92 n 92 GLY 92 A THR 93 n 93 THR 93 A VAL 94 n 94 VAL 94 A GLN 95 n 95 GLN 95 A GLY 96 n 96 GLY 96 A PHE 97 n 97 PHE 97 A LEU 98 n 98 LEU 98 A GLU 99 n 99 GLU 99 A LEU 100 n 100 LEU 100 A LEU 101 n 101 LEU 101 A GLY 102 n 102 GLY 102 A LYS 103 n 103 LYS 103 A PRO 104 n 104 PRO 104 A TYR 105 n 105 TYR 105 A VAL 106 n 106 VAL 106 A GLY 107 n 107 GLY 107 A ALA 108 n 108 ALA 108 A GLY 109 n 109 GLY 109 A VAL 110 n 110 VAL 110 A ALA 111 n 111 ALA 111 A ALA 112 n 112 ALA 112 A SER 113 n 113 SER 113 A ALA 114 n 114 ALA 114 A LEU 115 n 115 LEU 115 A CYS 116 n 116 CYS 116 A MET 117 n 117 MET 117 A ASP 118 n 118 ASP 118 A LYS 119 n 119 LYS 119 A ASP 120 n 120 ASP 120 A LEU 121 n 121 LEU 121 A SER 122 n 122 SER 122 A LYS 123 n 123 LYS 123 A ARG 124 n 124 ARG 124 A VAL 125 n 125 VAL 125 A LEU 126 n 126 LEU 126 A ALA 127 n 127 ALA 127 A GLN 128 n 128 GLN 128 A ALA 129 n 129 ALA 129 A GLY 130 n 130 GLY 130 A VAL 131 n 131 VAL 131 A PRO 132 n 132 PRO 132 A VAL 133 n 133 VAL 133 A VAL 134 n 134 VAL 134 A PRO 135 n 135 PRO 135 A TRP 136 n 136 TRP 136 A VAL 137 n 137 VAL 137 A ALA 138 n 138 ALA 138 A VAL 139 n 139 VAL 139 A ARG 140 n 140 ARG 140 A LYS 141 n 141 LYS 141 A GLY 142 n 142 GLY 142 A GLU 143 n 143 GLU 143 A PRO 144 n 144 PRO 144 A PRO 145 n 145 PRO 145 A VAL 146 n 146 VAL 146 A VAL 147 n 147 VAL 147 A PRO 148 n 148 PRO 148 A PHE 149 n 149 PHE 149 A ASP 150 n 150 ASP 150 A PRO 151 n 151 PRO 151 A PRO 152 n 152 PRO 152 A PHE 153 n 153 PHE 153 A PHE 154 n 154 PHE 154 A VAL 155 n 155 VAL 155 A LYS 156 n 156 LYS 156 A PRO 157 n 157 PRO 157 A ALA 158 n 158 ALA 158 A ASN 159 n 159 ASN 159 A THR 160 n 160 THR 160 A GLY 161 n 161 GLY 161 A SER 162 n 162 SER 162 A SER 163 n 163 SER 163 A VAL 164 n 164 VAL 164 A GLY 165 n 165 GLY 165 A ILE 166 n 166 ILE 166 A SER 167 n 167 SER 167 A ARG 168 n 168 ARG 168 A VAL 169 n 169 VAL 169 A GLU 170 n 170 GLU 170 A ARG 171 n 171 ARG 171 A PHE 172 n 172 PHE 172 A GLN 173 n 173 GLN 173 A ASP 174 n 174 ASP 174 A LEU 175 n 175 LEU 175 A GLU 176 n 176 GLU 176 A ALA 177 n 177 ALA 177 A ALA 178 n 178 ALA 178 A LEU 179 n 179 LEU 179 A ALA 180 n 180 ALA 180 A LEU 181 n 181 LEU 181 A ALA 182 n 182 ALA 182 A PHE 183 n 183 PHE 183 A ARG 184 n 184 ARG 184 A TYR 185 n 185 TYR 185 A ASP 186 n 186 ASP 186 A GLU 187 n 187 GLU 187 A LYS 188 n 188 LYS 188 A ALA 189 n 189 ALA 189 A VAL 190 n 190 VAL 190 A VAL 191 n 191 VAL 191 A GLU 192 n 192 GLU 192 A LYS 193 n 193 LYS 193 A ALA 194 n 194 ALA 194 A LEU 195 n 195 LEU 195 A SER 196 n 196 SER 196 A PRO 197 n 197 PRO 197 A VAL 198 n 198 VAL 198 A ARG 199 n 199 ARG 199 A GLU 200 n 200 GLU 200 A LEU 201 n 201 LEU 201 A GLU 202 n 202 GLU 202 A VAL 203 n 203 VAL 203 A GLY 204 n 204 GLY 204 A VAL 205 n 205 VAL 205 A LEU 206 n 206 LEU 206 A GLY 207 n 207 GLY 207 A ASN 208 n 208 ASN 208 A VAL 209 n 209 VAL 209 A PHE 210 n 210 PHE 210 A GLY 211 n 211 GLY 211 A GLU 212 n 212 GLU 212 A ALA 213 n 213 ALA 213 A SER 214 n 214 SER 214 A PRO 215 n 215 PRO 215 A VAL 216 n 216 VAL 216 A GLY 217 n 217 GLY 217 A GLU 218 n 218 GLU 218 A VAL 219 n 219 VAL 219 A ARG 220 n 220 ARG 220 A TYR 221 n 221 TYR 221 A GLU 222 n 222 GLU 222 A ALA 223 n 223 ALA 223 A PRO 224 n 224 PRO 224 A PHE 225 n 225 PHE 225 A TYR 226 n 226 TYR 226 A ASP 227 n 227 ASP 227 A TYR 228 n 228 TYR 228 A GLU 229 n 229 GLU 229 A THR 230 n 230 THR 230 A LYS 231 n 231 LYS 231 A TYR 232 n 232 TYR 232 A THR 233 n 233 THR 233 A PRO 234 n 234 PRO 234 A GLY 235 n 235 GLY 235 A ARG 236 n 236 ARG 236 A ALA 237 n 237 ALA 237 A GLU 238 n 238 GLU 238 A LEU 239 n 239 LEU 239 A LEU 240 n 240 LEU 240 A ILE 241 n 241 ILE 241 A PRO 242 n 242 PRO 242 A ALA 243 n 243 ALA 243 A PRO 244 n 244 PRO 244 A LEU 245 n 245 LEU 245 A ASP 246 n 246 ASP 246 A PRO 247 n 247 PRO 247 A GLY 248 n 248 GLY 248 A THR 249 n 249 THR 249 A GLN 250 n 250 GLN 250 A GLU 251 n 251 GLU 251 A THR 252 n 252 THR 252 A VAL 253 n 253 VAL 253 A GLN 254 n 254 GLN 254 A GLU 255 n 255 GLU 255 A LEU 256 n 256 LEU 256 A ALA 257 n 257 ALA 257 A LEU 258 n 258 LEU 258 A LYS 259 n 259 LYS 259 A ALA 260 n 260 ALA 260 A TYR 261 n 261 TYR 261 A LYS 262 n 262 LYS 262 A VAL 263 n 263 VAL 263 A LEU 264 n 264 LEU 264 A GLY 265 n 265 GLY 265 A VAL 266 n 266 VAL 266 A ARG 267 n 267 ARG 267 A GLY 268 n 268 GLY 268 A MET 269 n 269 MET 269 A ALA 270 n 270 ALA 270 A ARG 271 n 271 ARG 271 A VAL 272 n 272 VAL 272 A ASP 273 n 273 ASP 273 A PHE 274 n 274 PHE 274 A PHE 275 n 275 PHE 275 A LEU 276 n 276 LEU 276 A ALA 277 n 277 ALA 277 A GLU 278 n 278 GLU 278 A GLY 279 n 279 GLY 279 A GLU 280 n 280 GLU 280 A LEU 281 n 281 LEU 281 A TYR 282 n 282 TYR 282 A LEU 283 n 283 LEU 283 A ASN 284 n 284 ASN 284 A GLU 285 n 285 GLU 285 A LEU 286 n 286 LEU 286 A ASN 287 n 287 ASN 287 A THR 288 n 288 THR 288 A ILE 289 n 289 ILE 289 A PRO 290 n 290 PRO 290 A GLY 291 n 291 GLY 291 A PHE 292 n 292 PHE 292 A THR 293 n 293 THR 293 A PRO 294 n 294 PRO 294 A THR 295 n 295 THR 295 A SER 296 n 296 SER 296 A MET 297 n 297 MET 297 A TYR 298 n 298 TYR 298 A PRO 299 n 299 PRO 299 A ARG 300 n 300 ARG 300 A LEU 301 n 301 LEU 301 A PHE 302 n 302 PHE 302 A GLU 303 n 303 GLU 303 A ALA 304 n 304 ALA 304 A GLY 305 n 305 GLY 305 A GLY 306 n 306 GLY 306 A VAL 307 n 307 VAL 307 A ALA 308 n 308 ALA 308 A TYR 309 n 309 TYR 309 A PRO 310 n 310 PRO 310 A GLU 311 n 311 GLU 311 A LEU 312 n 312 LEU 312 A LEU 313 n 313 LEU 313 A ARG 314 n 314 ARG 314 A ARG 315 n 315 ARG 315 A LEU 316 n 316 LEU 316 A VAL 317 n 317 VAL 317 A GLU 318 n 318 GLU 318 A LEU 319 n 319 LEU 319 A ALA 320 n 320 ALA 320 A LEU 321 n 321 LEU 321 A THR 322 n 322 THR 322 A author_and_software_defined_assembly PISA,PQS 2 dimeric 2740 -22 27930 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_755 -x+2,y,-z+1/2 crystal symmetry operation 230.4320000000 0.0000000000 29.6620000000 A O LEU 47 A O LEU 47 A N VAL 39 A N VAL 39 A O ASP 36 A O ASP 36 A N LEU 8 A N LEU 8 A N LEU 7 A N LEU 7 A O PHE 81 A O PHE 81 A N VAL 139 A N VAL 139 A O ALA 189 A O ALA 189 A O GLU 192 A O GLU 192 A N PHE 154 A N PHE 154 A N VAL 155 A N VAL 155 A O SER 167 A O SER 167 A O GLU 238 A O GLU 238 A N ARG 220 A N ARG 220 A O GLY 217 A O GLY 217 A N GLU 202 A N GLU 202 A N LEU 201 A N LEU 201 A O PHE 274 A O PHE 274 A N ASP 273 A N ASP 273 A O GLU 285 A O GLU 285 A N ASP 227 A N ASP 227 A O LYS 231 A O LYS 231 1 A PRO 32 -65.78 15.77 1 A GLU 63 -50.39 -112.43 1 A PHE 68 -9.17 -92.89 1 A PRO 69 -49.34 90.54 1 A TRP 74 58.81 -45.55 1 A ASP 150 -41.73 157.35 1 A VAL 198 64.70 141.33 1 A VAL 209 67.65 -56.35 1 A LYS 231 63.40 -141.11 1 A ALA 270 -178.07 143.42 0.268 0.228 0.249 0.232 1.9 30 3379 33979 24867 RANDOM 1 2 MOLECULAR REPLACEMENT Engh & Huber 1.9 30 115 2596 0 0 2481 1.9 50 2FB9 25640 2.0 2.0 1 85 1.9 1.96 1 97 data collection HKL-2000 data scaling SCALEPACK phasing AMoRE refinement CNS 1.1 data reduction HKL-2000 Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes 1 N N 2 N N Biological unit is dimer A GLU 16 A GLU 16 HELX_P A ILE 31 A ILE 31 1 1 16 A LEU 48 A LEU 48 HELX_P A LEU 56 A LEU 56 1 2 9 A GLY 92 A GLY 92 HELX_P A GLY 102 A GLY 102 1 3 11 A GLY 109 A GLY 109 HELX_P A ASP 118 A ASP 118 1 4 10 A ASP 118 A ASP 118 HELX_P A ALA 129 A ALA 129 1 5 12 A ARG 171 A ARG 171 HELX_P A PHE 183 A PHE 183 1 6 13 A GLY 248 A GLY 248 HELX_P A GLY 265 A GLY 265 1 7 18 A SER 296 A SER 296 HELX_P A GLY 305 A GLY 305 1 8 10 A ALA 308 A ALA 308 HELX_P A LEU 321 A LEU 321 1 9 14 LIGASE ligase A SER 196 A SER 196 1 A PRO 197 A PRO 197 0.21 A ILE 241 A ILE 241 1 A PRO 242 A PRO 242 -0.06 Q3T920_THECA UNP 1 1 Q3T920 1 319 2FB9 4 322 Q3T920 A 1 4 322 1 cloning artifact MET 1 2FB9 A Q3T920 UNP 1 1 cloning artifact GLU 2 2FB9 A Q3T920 UNP 2 1 cloning artifact PHE 3 2FB9 A Q3T920 UNP 3 4 4 5 2 anti-parallel parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TRP 46 A TRP 46 A LEU 47 A LEU 47 A THR 35 A THR 35 A ILE 40 A ILE 40 A VAL 6 A VAL 6 A GLY 11 A GLY 11 A VAL 79 A VAL 79 A LEU 83 A LEU 83 A TRP 136 A TRP 136 A ARG 140 A ARG 140 A LYS 188 A LYS 188 A LYS 193 A LYS 193 A PHE 153 A PHE 153 A PRO 157 A PRO 157 A SER 167 A SER 167 A VAL 169 A VAL 169 A ARG 236 A ARG 236 A LEU 240 A LEU 240 A GLU 212 A GLU 212 A GLU 222 A GLU 222 A ARG 199 A ARG 199 A LEU 206 A LEU 206 A MET 269 A MET 269 A ALA 277 A ALA 277 A GLU 280 A GLU 280 A ASN 287 A ASN 287 A PHE 225 A PHE 225 A ASP 227 A ASP 227 A LYS 231 A LYS 231 A THR 233 A THR 233 20 C 2 2 21