0.005569 0.000000 0.000000 0.000000 0.005569 0.000000 0.000000 0.000000 0.022801 0.00000 0.00000 0.00000 Yin, L. 0000-0003-4175-3714 Shi, K. 0000-0001-7508-6230 Aihara, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 179.565 179.565 43.858 C2 H3 O2 -1 59.044 ACETATE ION non-polymer 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 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA 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 Zn 2 65.409 ZINC ION non-polymer N 1 N C N 2 N O N 3 N O N 4 N C N 5 N H N 6 N H N 7 N H N 8 N N N 9 S C N 10 N C N 11 N O N 12 N C N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N N N 22 S C N 23 N C N 24 N O N 25 N C N 26 N C N 27 N C N 28 N N N 29 N C N 30 N N N 31 N N N 32 N O 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 H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N N N 49 S C N 50 N C N 51 N O N 52 N C N 53 N C N 54 N O N 55 N N N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N N N 66 S C N 67 N C N 68 N O N 69 N C N 70 N C N 71 N O N 72 N O N 73 N O N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N N N 82 R C N 83 N C N 84 N O N 85 N C N 86 N S N 87 N O 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 H N 95 N O N 96 N P N 97 N O N 98 N O N 99 N O N 100 N C N 101 R C N 102 N O N 103 S C N 104 N O N 105 N C N 106 R C Y 107 N N Y 108 N C Y 109 N N Y 110 N C Y 111 N C N 112 N N Y 113 N N Y 114 N C Y 115 N N Y 116 N C N 117 N H 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 H N 128 N H N 129 N H N 130 N H N 131 N O N 132 N P N 133 N O N 134 N O N 135 N O N 136 N C N 137 R C N 138 N O N 139 S C N 140 N O N 141 N C N 142 R C N 143 N N N 144 N C N 145 N O N 146 N N N 147 N C N 148 N N N 149 N C N 150 N C 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 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 O N 166 N P N 167 N O N 168 N O N 169 N O N 170 N C N 171 R C N 172 N O N 173 S C N 174 N O N 175 N C N 176 R C Y 177 N N Y 178 N C Y 179 N N Y 180 N C N 181 N C N 182 N O N 183 N N N 184 N C N 185 N N N 186 N N Y 187 N C N 188 N H N 189 N H N 190 N H N 191 N H 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 O N 203 N P N 204 N O N 205 N O N 206 N O N 207 N C N 208 R C N 209 N O N 210 S C N 211 N O N 212 N C N 213 R C N 214 N N N 215 N C N 216 N O N 217 N N N 218 N C N 219 N O N 220 N C N 221 N C N 222 N C 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 H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N N N 239 S C N 240 N C N 241 N O N 242 N C N 243 N C N 244 N C N 245 N O N 246 N N N 247 N O 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 H N 255 N H N 256 N H N 257 N H N 258 N N N 259 S C N 260 N C N 261 N O N 262 N C N 263 N C N 264 N C N 265 N O N 266 N O N 267 N O 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 N N 278 N C N 279 N C N 280 N O N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N N N 288 S C N 289 N C N 290 N O N 291 N C Y 292 N C Y 293 N N Y 294 N C Y 295 N C Y 296 N N N 297 N O 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 H N 305 N H N 306 N H N 307 N H N 308 N O N 309 N H N 310 N H N 311 N N N 312 S C N 313 N C N 314 N O N 315 S C N 316 N C N 317 N C N 318 N C N 319 N O N 320 N H 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 H N 331 N H N 332 N H N 333 N N N 334 S C N 335 N C N 336 N O N 337 N C N 338 N C N 339 N C N 340 N C N 341 N O 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 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 N N 356 S C N 357 N C N 358 N O N 359 N C N 360 N C N 361 N C N 362 N C N 363 N N N 364 N O 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 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 N N 381 S C N 382 N C N 383 N O N 384 N C N 385 N C N 386 N S 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 400 N N N 401 S C N 402 N C N 403 N O N 404 N C Y 405 N C Y 406 N C Y 407 N C Y 408 N C Y 409 N C Y 410 N C N 411 N O N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 N H N 423 N N N 424 S C N 425 N C N 426 N O N 427 N C N 428 N C N 429 N C N 430 N O N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N N N 441 S C N 442 N C N 443 N O N 444 N C N 445 N O N 446 N O N 447 N H N 448 N H N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N N N 455 S C N 456 N C N 457 N O N 458 R C N 459 N O N 460 N C N 461 N O N 462 N H N 463 N H N 464 N H N 465 N H N 466 N H N 467 N H N 468 N H N 469 N H N 470 N H N 471 N N N 472 S C N 473 N C N 474 N O N 475 N C Y 476 N C Y 477 N C Y 478 N C Y 479 N N Y 480 N C Y 481 N C Y 482 N C Y 483 N C Y 484 N C N 485 N O N 486 N H N 487 N H N 488 N H N 489 N H N 490 N H N 491 N H N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 N H N 498 N N N 499 S C N 500 N C N 501 N O N 502 N C Y 503 N C Y 504 N C Y 505 N C Y 506 N C Y 507 N C Y 508 N C N 509 N O N 510 N O N 511 N H N 512 N H N 513 N H N 514 N H N 515 N H N 516 N H N 517 N H N 518 N H N 519 N H N 520 N H N 521 N H N 522 N N N 523 S C N 524 N C N 525 N O N 526 N C N 527 N C N 528 N C N 529 N O N 530 N H N 531 N H N 532 N H N 533 N H N 534 N H N 535 N H N 536 N H N 537 N H N 538 N H N 539 N H N 540 N H N 541 N ZN N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N doub 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 sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N doub N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N doub N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N doub N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N doub 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 sing N 90 N sing N 91 N doub N 92 N sing N 93 N sing N 94 N sing N 95 N sing 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 sing 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 Y 112 N sing Y 113 N sing Y 114 N doub N 115 N sing Y 116 N sing Y 117 N sing Y 118 N doub N 119 N sing Y 120 N doub N 121 N sing N 122 N sing Y 123 N sing Y 124 N doub N 125 N sing Y 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 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 sing 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 doub N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N doub N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N doub 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 sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing Y 185 N sing Y 186 N sing Y 187 N doub N 188 N sing Y 189 N sing N 190 N sing Y 191 N doub N 192 N doub N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N doub N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub 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 sing N 225 N sing N 226 N doub N 227 N sing N 228 N sing N 229 N sing N 230 N doub N 231 N sing N 232 N sing N 233 N doub 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 doub N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N doub N 253 N sing N 254 N sing N 255 N sing N 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 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 doub 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 doub 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 Y 295 N sing Y 296 N doub Y 297 N doub N 298 N sing Y 299 N sing N 300 N sing Y 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 sing N 313 N doub N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N doub N 335 N sing N 336 N sing N 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 sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N doub 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 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 sing 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 doub N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N doub N 399 N sing N 400 N sing N 401 N sing N 402 N sing Y 403 N doub Y 404 N sing Y 405 N sing N 406 N sing Y 407 N doub N 408 N sing Y 409 N doub N 410 N sing Y 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N doub N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N doub N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N doub N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N doub N 468 N sing N 469 N sing N 470 N sing N 471 N sing Y 472 N doub Y 473 N sing Y 474 N sing N 475 N sing Y 476 N doub Y 477 N sing Y 478 N sing N 479 N sing Y 480 N sing Y 481 N doub N 482 N sing Y 483 N doub N 484 N sing Y 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N sing N 490 N sing N 491 N sing N 492 N sing N 493 N sing N 494 N sing N 495 N doub N 496 N sing N 497 N sing N 498 N sing N 499 N sing Y 500 N doub Y 501 N sing Y 502 N sing N 503 N sing Y 504 N doub N 505 N sing Y 506 N doub N 507 N sing Y 508 N sing N 509 N sing N 510 N sing N 511 N sing N 512 N sing N 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N sing N 519 N doub N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N sing N 525 N sing N 526 N sing N 527 N sing N 528 N sing N 529 N sing N 530 N sing To Be Published 0353 Structural Basis of double-stranded DNA cytosine deamination with relaxed sequence dependence by a BaDTF3 toxin DddB 10.2210/pdb9pw1/pdb pdb_00009pw1 100 1 N PIXEL 2023-12-02 DECTRIS EIGER X 9M SINGLE WAVELENGTH M x-ray 1 0.92009 1.0 17-ID-1 NSLS-II 0.92009 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 11591.220 BaDTF3 1 man polymer 4280.792 DNA substrate 1 syn polymer 4280.792 DNA substrate 1 syn polymer 65.409 ZINC ION 1 syn non-polymer 59.044 ACETATE ION 1 syn non-polymer 18.015 water 3 nat water no no MHKATVTVTDKNGVVKHKSNLVSGNMTEAEKKLGFPNNSLATHTANRATRLIDLNQGDTMLIEGQYRPCPRCKGAMRVKA EESGAKVIYTWPEDGDLKKREWEG MHKATVTVTDKNGVVKHKSNLVSGNMTEAEKKLGFPNNSLATHTANRATRLIDLNQGDTMLIEGQYRPCPRCKGAMRVKA EESGAKVIYTWPEDGDLKKREWEG A polypeptide(L) no no (DG)(DC)(DA)(DA)(DG)(DT)(DT)(DC)(DG)(DG)(DC)(DT)(DA)(DC) GCAAGTTCGGCTAC E polydeoxyribonucleotide no no (DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DA)(DC)(DT)(DT)(DG)(DC) GTAGCCGAACTTGC F polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 1 104 29575 Taylorella equigenitalis 562 Escherichia coli Biological sequence 1 4.39 71.95 VAPOR DIFFUSION, SITTING DROP J000778, C01_10 0.2 M, Magnesium acetate, 20 % w/v, Polyethylene glycol 3350, pH 7.9 295 -1.726 1 19 E 1 F 14 2.109 E_DG1:DC14_F 1 1.109 -0.218 -0.398 -0.084 6.587 1 19 E 2 F 13 -0.310 E_DC2:DG13_F 2 -0.128 0.178 0.242 -0.139 9.344 1 20 E 3 F 12 1.806 E_DA3:DT12_F 3 -10.015 0.195 0.656 -0.109 1.973 1 20 E 4 F 11 -0.798 E_DA4:DT11_F 4 -7.650 0.077 0.318 0.074 3.959 1 19 E 5 F 10 3.686 E_DG5:DC10_F 5 -10.321 -0.164 0.464 -0.057 0.199 1 20 E 6 F 9 7.642 E_DT6:DA9_F 6 -0.574 -0.235 0.156 -0.107 11.815 1 20 E 7 F 8 -0.096 E_DT7:DA8_F 7 4.020 -0.240 -0.074 0.084 -21.164 1 19 E 9 F 6 -0.674 E_DG9:DC6_F 8 -1.419 0.018 -0.991 -0.112 -2.992 1 19 E 10 F 5 -1.129 E_DG10:DC5_F 9 1.734 -0.074 -0.446 -0.109 -0.746 1 19 E 11 F 4 -1.535 E_DC11:DG4_F 10 -8.236 0.165 0.269 -0.133 -3.522 1 20 E 12 F 3 -3.493 E_DT12:DA3_F 11 -11.133 -0.116 0.403 0.011 13.725 1 20 E 13 F 2 -6.516 E_DA13:DT2_F 12 2.171 0.331 1.527 -0.093 3.215 1 19 E 14 F 1 2.017 E_DC14:DG1_F 13 0.885 0.238 0.812 -0.167 3.045 30.324 E E 1 2 5.290 F F 14 13 3.067 2.756 -0.072 0.088 EE_DG1DC2:DG13DC14_FF 1 -4.118 7.906 29.926 -0.354 -0.643 3.126 38.218 E E 2 3 6.644 F F 13 12 3.114 4.338 -0.248 0.195 EE_DC2DA3:DT12DG13_FF 2 -2.864 4.388 37.876 -0.226 0.033 3.496 36.013 E E 3 4 -7.693 F F 12 11 3.443 -4.743 -0.038 -0.641 EE_DA3DA4:DT11DT12_FF 3 0.558 -0.905 35.706 -0.319 0.145 3.083 35.412 E E 4 5 2.630 F F 11 10 3.197 1.595 0.416 -0.762 EE_DA4DG5:DC10DT11_FF 4 -4.572 7.539 35.090 -1.479 -1.333 3.446 34.764 E E 5 6 -1.039 F F 10 9 3.452 -0.620 0.056 -0.541 EE_DG5DT6:DA9DC10_FF 5 3.921 -6.576 34.543 -0.805 0.540 3.028 21.030 E E 6 7 16.017 F F 9 8 3.131 5.770 -0.690 0.210 EE_DT6DT7:DA8DA9_FF 6 1.153 -3.202 20.199 -1.761 2.358 2.931 26.292 E E 9 10 12.805 F F 6 5 2.927 5.730 -0.010 0.673 EE_DG9DG10:DC5DC6_FF 7 -5.910 13.208 24.992 0.064 -1.437 3.215 36.433 E E 10 11 1.144 F F 5 4 3.100 0.712 -0.976 0.126 EE_DG10DC11:DG4DC5_FF 8 -5.774 9.272 35.981 0.105 0.782 3.226 33.005 E E 11 12 3.909 F F 4 3 3.288 2.218 -0.328 -0.517 EE_DC11DT12:DA3DG4_FF 9 1.750 -3.084 32.887 -1.286 0.873 2.611 47.317 E E 12 13 -12.736 F F 3 2 2.942 -10.121 0.980 0.579 EE_DT12DA13:DT2DA3_FF 10 -6.486 8.162 45.849 1.432 -1.677 3.750 31.730 E E 13 14 -4.127 F F 2 1 3.626 -2.243 0.632 -1.138 EE_DA13DC14:DG1DT2_FF 11 5.790 -10.656 31.132 -1.612 0.055 repository Initial release 1 0 2026-08-05 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM118047 aihar001@umn.edu 0000-0001-7508-6230 Hideki Aihara principal investigator/group leader N RCSB Y RCSB 2025-08-04 REL REL ZN ZINC ION ACT ACETATE ION HOH water 29575 Taylorella equigenitalis sample 1 14 29575 Taylorella equigenitalis sample 1 14 N N AlphaFold in silico model ZN 2117 4 ZN ZN 2101 A ACT 101 5 ACT ACT 101 F HOH 1 6 HOH HOH 101 E HOH 3 6 HOH HOH 102 E HOH 2 6 HOH HOH 103 E MET 1951 n 1 MET 1951 A HIS 1952 n 2 HIS 1952 A LYS 1953 n 3 LYS 1953 A ALA 1954 n 4 ALA 1954 A THR 1955 n 5 THR 1955 A VAL 1956 n 6 VAL 1956 A THR 1957 n 7 THR 1957 A VAL 1958 n 8 VAL 1958 A THR 1959 n 9 THR 1959 A ASP 1960 n 10 ASP 1960 A LYS 1961 n 11 LYS 1961 A ASN 1962 n 12 ASN 1962 A GLY 1963 n 13 GLY 1963 A VAL 1964 n 14 VAL 1964 A VAL 1965 n 15 VAL 1965 A LYS 1966 n 16 LYS 1966 A HIS 1967 n 17 HIS 1967 A LYS 1968 n 18 LYS 1968 A SER 1969 n 19 SER 1969 A ASN 1970 n 20 ASN 1970 A LEU 1971 n 21 LEU 1971 A VAL 1972 n 22 VAL 1972 A SER 1973 n 23 SER 1973 A GLY 1974 n 24 GLY 1974 A ASN 1975 n 25 ASN 1975 A MET 1976 n 26 MET 1976 A THR 1977 n 27 THR 1977 A GLU 1978 n 28 GLU 1978 A ALA 1979 n 29 ALA 1979 A GLU 1980 n 30 GLU 1980 A LYS 1981 n 31 LYS 1981 A LYS 1982 n 32 LYS 1982 A LEU 1983 n 33 LEU 1983 A GLY 1984 n 34 GLY 1984 A PHE 1985 n 35 PHE 1985 A PRO 1986 n 36 PRO 1986 A ASN 1987 n 37 ASN 1987 A ASN 1988 n 38 ASN 1988 A SER 1989 n 39 SER 1989 A LEU 1990 n 40 LEU 1990 A ALA 1991 n 41 ALA 1991 A THR 1992 n 42 THR 1992 A HIS 1993 n 43 HIS 1993 A THR 1994 n 44 THR 1994 A ALA 1995 n 45 ALA 1995 A ASN 1996 n 46 ASN 1996 A ARG 1997 n 47 ARG 1997 A ALA 1998 n 48 ALA 1998 A THR 1999 n 49 THR 1999 A ARG 2000 n 50 ARG 2000 A LEU 2001 n 51 LEU 2001 A ILE 2002 n 52 ILE 2002 A ASP 2003 n 53 ASP 2003 A LEU 2004 n 54 LEU 2004 A ASN 2005 n 55 ASN 2005 A GLN 2006 n 56 GLN 2006 A GLY 2007 n 57 GLY 2007 A ASP 2008 n 58 ASP 2008 A THR 2009 n 59 THR 2009 A MET 2010 n 60 MET 2010 A LEU 2011 n 61 LEU 2011 A ILE 2012 n 62 ILE 2012 A GLU 2013 n 63 GLU 2013 A GLY 2014 n 64 GLY 2014 A GLN 2015 n 65 GLN 2015 A TYR 2016 n 66 TYR 2016 A ARG 2017 n 67 ARG 2017 A PRO 2018 n 68 PRO 2018 A CYS 2019 n 69 CYS 2019 A PRO 2020 n 70 PRO 2020 A ARG 2021 n 71 ARG 2021 A CYS 2022 n 72 CYS 2022 A LYS 2023 n 73 LYS 2023 A GLY 2024 n 74 GLY 2024 A ALA 2025 n 75 ALA 2025 A MET 2026 n 76 MET 2026 A ARG 2027 n 77 ARG 2027 A VAL 2028 n 78 VAL 2028 A LYS 2029 n 79 LYS 2029 A ALA 2030 n 80 ALA 2030 A GLU 2031 n 81 GLU 2031 A GLU 2032 n 82 GLU 2032 A SER 2033 n 83 SER 2033 A GLY 2034 n 84 GLY 2034 A ALA 2035 n 85 ALA 2035 A LYS 2036 n 86 LYS 2036 A VAL 2037 n 87 VAL 2037 A ILE 2038 n 88 ILE 2038 A TYR 2039 n 89 TYR 2039 A THR 2040 n 90 THR 2040 A TRP 2041 n 91 TRP 2041 A PRO 2042 n 92 PRO 2042 A GLU 2043 n 93 GLU 2043 A ASP 2044 n 94 ASP 2044 A GLY 2045 n 95 GLY 2045 A ASP 2046 n 96 ASP 2046 A LEU 2047 n 97 LEU 2047 A LYS 2048 n 98 LYS 2048 A LYS 2049 n 99 LYS 2049 A ARG 2050 n 100 ARG 2050 A GLU 2051 n 101 GLU 2051 A TRP 2052 n 102 TRP 2052 A GLU 2053 n 103 GLU 2053 A GLY 2054 n 104 GLY 2054 A DG 1 n 1 DG 1 E DC 2 n 2 DC 2 E DA 3 n 3 DA 3 E DA 4 n 4 DA 4 E DG 5 n 5 DG 5 E DT 6 n 6 DT 6 E DT 7 n 7 DT 7 E DC 8 n 8 DC 8 E DG 9 n 9 DG 9 E DG 10 n 10 DG 10 E DC 11 n 11 DC 11 E DT 12 n 12 DT 12 E DA 13 n 13 DA 13 E DC 14 n 14 DC 14 E DG 1 n 1 DG 1 F DT 2 n 2 DT 2 F DA 3 n 3 DA 3 F DG 4 n 4 DG 4 F DC 5 n 5 DC 5 F DC 6 n 6 DC 6 F DG 7 n 7 DG 7 F DA 8 n 8 DA 8 F DA 9 n 9 DA 9 F DC 10 n 10 DC 10 F DT 11 n 11 DT 11 F DT 12 n 12 DT 12 F DG 13 n 13 DG 13 F DC 14 n 14 DC 14 F 4.6350 3.0683 -1.0088 3.8949 2.6624 9.3013 0.0773 -0.8975 0.4551 0.2321 0.0751 0.4639 1.0630 1.3117 0.2649 0.9707 -0.1689 0.1443 0.6965 0.1100 1.1685 refined 28.6115 -15.8326 22.6265 X-RAY DIFFRACTION 1.9913 1.0805 0.0946 4.6111 0.3120 7.6630 -1.0858 0.9346 1.7271 -0.1194 0.1480 1.2173 -0.2166 -1.1359 0.5733 0.7991 -0.2810 -0.0274 0.8026 0.1830 1.5800 refined 18.7240 -14.4815 18.4114 X-RAY DIFFRACTION 8.9700 2.3398 -5.0560 2.7226 1.8417 7.5322 -0.4736 0.6375 -1.7128 -0.0963 -0.5639 -0.2960 0.6104 -0.8598 0.6124 1.3599 0.2585 0.1417 0.7382 0.2668 1.2780 refined 38.6234 -29.8862 15.4580 X-RAY DIFFRACTION 8.6610 2.4625 -3.5426 2.7949 2.0103 5.7436 -0.9303 0.6158 -0.0055 -0.1058 0.9242 0.0116 1.6016 0.2832 0.3293 0.9739 0.0047 -0.0611 0.7165 0.2474 0.9192 refined 35.2322 -21.8436 14.5587 X-RAY DIFFRACTION 6.9787 -5.8522 3.1441 5.1834 -1.1723 9.4682 0.6011 1.9439 -1.2561 -0.9471 -0.6451 2.3065 0.5084 -1.2776 -0.0454 1.0742 -0.3052 -0.2505 1.1174 0.5231 1.6527 refined 19.9898 -14.4628 8.6025 X-RAY DIFFRACTION 4.0761 -2.2174 0.8130 4.1724 3.3307 8.9615 0.0991 0.7056 0.1251 0.5443 -0.4426 0.7208 -0.2762 -2.0372 -0.0666 0.6788 0.0417 0.0090 0.4937 0.2782 1.0518 refined 26.6366 -10.8042 18.6360 X-RAY DIFFRACTION 5.7554 -1.3639 -1.8100 9.2366 4.6818 8.5869 0.6925 -1.0739 -0.3957 0.6254 -0.6578 0.5355 0.9316 1.1475 -0.1590 0.5494 0.0208 -0.1868 0.5815 0.3249 0.9603 refined 39.7913 -11.8995 21.1432 X-RAY DIFFRACTION 5.8389 -1.3713 -1.0516 6.9615 1.6911 4.8486 0.2291 1.2287 0.2940 -0.1888 -0.2125 0.6360 0.5144 -0.5147 -0.0990 0.6094 -0.0615 -0.1298 0.6713 0.3434 0.8673 refined 32.6895 -10.4300 12.0732 X-RAY DIFFRACTION 4.7021 0.6908 -1.2020 7.0180 3.3127 2.0891 -0.9145 0.7938 0.3888 -0.5931 0.2658 0.1182 -0.4725 -0.1570 -0.6196 0.6235 0.1260 0.0256 0.5596 0.3915 1.0993 refined 33.6836 -3.1378 17.5128 X-RAY DIFFRACTION 0.8266 -0.3105 0.7963 4.3154 -0.3395 0.7103 -0.1390 -0.2424 -0.4422 -0.4327 -0.2354 -0.7709 1.7344 1.2336 0.4329 1.3089 0.5059 -0.0385 1.1298 0.2908 1.0398 refined 50.4408 -20.0259 14.8644 X-RAY DIFFRACTION 5.0480 -2.6734 2.4338 5.6987 -3.0494 8.5237 0.6413 -0.2087 -0.5675 0.0027 -0.7204 -0.9492 1.9478 1.6190 0.1853 1.2811 0.2669 -0.0702 1.1477 0.3277 1.1202 refined 50.2959 -18.4699 14.4746 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resid 1951 through 1959 ) X-RAY DIFFRACTION 2 chain 'A' and (resid 1960 through 1972 ) X-RAY DIFFRACTION 3 chain 'A' and (resid 1973 through 1986 ) X-RAY DIFFRACTION 4 chain 'A' and (resid 1987 through 2001 ) X-RAY DIFFRACTION 5 chain 'A' and (resid 2002 through 2008 ) X-RAY DIFFRACTION 6 chain 'A' and (resid 2009 through 2014 ) X-RAY DIFFRACTION 7 chain 'A' and (resid 2015 through 2019 ) X-RAY DIFFRACTION 8 chain 'A' and (resid 2020 through 2043 ) X-RAY DIFFRACTION 9 chain 'A' and (resid 2044 through 2054 ) X-RAY DIFFRACTION 10 chain 'E' and (resid 1 through 14 ) X-RAY DIFFRACTION 11 chain 'F' and (resid 1 through 14 ) author_and_software_defined_assembly PISA 3 trimeric gel filtration 3630 -57 9700 A HIS 1993 A ND1 HIS 43 1_555 A ZN 2101 D ZN ZN 1_555 A CYS 2019 A SG CYS 69 1_555 117.8 A HIS 1993 A ND1 HIS 43 1_555 A ZN 2101 D ZN ZN 1_555 A CYS 2022 A SG CYS 72 1_555 123.5 A CYS 2019 A SG CYS 69 1_555 A ZN 2101 D ZN ZN 1_555 A CYS 2022 A SG CYS 72 1_555 107.3 A HIS 1993 A ND1 HIS 43 1_555 A ZN 2101 D ZN ZN 1_555 E HOH 101 F O HOH 1_555 115.0 A CYS 2019 A SG CYS 69 1_555 A ZN 2101 D ZN ZN 1_555 E HOH 101 F O HOH 1_555 96.2 A CYS 2022 A SG CYS 72 1_555 A ZN 2101 D ZN ZN 1_555 E HOH 101 F O HOH 1_555 90.7 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 O LEU 1971 A O LEU 21 A N ALA 1954 A N ALA 4 A N THR 1957 A N THR 7 A O LEU 2011 A O LEU 61 A N ILE 2012 A N ILE 62 A O ILE 2038 A O ILE 88 A N TYR 2039 A N TYR 89 A O ARG 2050 A O ARG 100 1 A A O ND2 GLU ASN 1980 1988 2.15 1 2.85 0.30 108.30 111.15 E E E O4' C1' N1 DT DT DT 7 7 7 N 1 1.89 0.30 108.30 110.19 E E E O4' C1' N1 DC DC DC 8 8 8 N 1 1.85 0.30 108.30 110.15 F F F O4' C1' N1 DC DC DC 10 10 10 N 1 F F O3' C3' DG DG 7 7 -0.037 0.006 1.419 1.382 N 1 E F OP2 O5' DC DG 14 1 1.94 1_555 15_546 1 A ASN 1975 55.44 70.56 0.2273 0.1932 0.1948 2.91 42.61 373 7356 5.07 90.05 0.39 1 FREE R-VALUE 1.35 MOLECULAR REPLACEMENT 26.06 0.90 1.10 ML FLAT BULK SOLVENT MODEL 2.91 42.61 3 1384 5 568 808 25.598 587 0.056 231 0.010 172 0.3108 0.2868 3.34 96 1743 70.00 0.2779 0.2259 4.20 139 2551 100.00 0.1910 0.1678 42.61 138 2689 100.00 2.91 126.972 9PW1 7362 0.167 0.048 0.174 1 9.9 13.6 90.1 3.323 2.914 3.065 5361 368 0.898 3.443 1 0.8 14.6 33.3 refinement PHENIX (1.20.1_4487: ???) data scaling Aimless data reduction XDS phasing PHASER N Crystal structure of Taylorella equigenitalis BaDTF3 deaminase toxin DddB (N-terminally truncated) bound to double-stranded DNA 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N A THR 1977 A THR 27 HELX_P A LYS 1982 A LYS 32 1 AA1 6 A PRO 1986 A PRO 36 HELX_P A HIS 1993 A HIS 43 1 AA2 8 A HIS 1993 A HIS 43 HELX_P A ILE 2002 A ILE 52 1 AA3 10 A CYS 2019 A CYS 69 HELX_P A GLY 2034 A GLY 84 1 AA4 16 metalc 2.053 A HIS 1993 A ND1 HIS 43 1_555 A ZN 2101 D ZN ZN 1_555 metalc 2.160 A CYS 2019 A SG CYS 69 1_555 A ZN 2101 D ZN ZN 1_555 metalc 2.110 A CYS 2022 A SG CYS 72 1_555 A ZN 2101 D ZN ZN 1_555 metalc 2.020 A ZN 2101 D ZN ZN 1_555 E HOH 101 F O HOH 1_555 hydrog WATSON-CRICK E DG 1 B N1 DG 1 1_555 F DC 14 C N3 DC 14 1_555 hydrog WATSON-CRICK E DG 1 B N2 DG 1 1_555 F DC 14 C O2 DC 14 1_555 hydrog WATSON-CRICK E DG 1 B O6 DG 1 1_555 F DC 14 C N4 DC 14 1_555 hydrog WATSON-CRICK E DC 2 B N3 DC 2 1_555 F DG 13 C N1 DG 13 1_555 hydrog WATSON-CRICK E DC 2 B N4 DC 2 1_555 F DG 13 C O6 DG 13 1_555 hydrog WATSON-CRICK E DC 2 B O2 DC 2 1_555 F DG 13 C N2 DG 13 1_555 hydrog WATSON-CRICK E DA 3 B N1 DA 3 1_555 F DT 12 C N3 DT 12 1_555 hydrog WATSON-CRICK E DA 3 B N6 DA 3 1_555 F DT 12 C O4 DT 12 1_555 hydrog WATSON-CRICK E DA 4 B N1 DA 4 1_555 F DT 11 C N3 DT 11 1_555 hydrog WATSON-CRICK E DA 4 B N6 DA 4 1_555 F DT 11 C O4 DT 11 1_555 hydrog WATSON-CRICK E DG 5 B N1 DG 5 1_555 F DC 10 C N3 DC 10 1_555 hydrog WATSON-CRICK E DG 5 B N2 DG 5 1_555 F DC 10 C O2 DC 10 1_555 hydrog WATSON-CRICK E DG 5 B O6 DG 5 1_555 F DC 10 C N4 DC 10 1_555 hydrog WATSON-CRICK E DT 6 B N3 DT 6 1_555 F DA 9 C N1 DA 9 1_555 hydrog WATSON-CRICK E DT 6 B O4 DT 6 1_555 F DA 9 C N6 DA 9 1_555 hydrog WATSON-CRICK E DT 7 B N3 DT 7 1_555 F DA 8 C N1 DA 8 1_555 hydrog WATSON-CRICK E DT 7 B O4 DT 7 1_555 F DA 8 C N6 DA 8 1_555 hydrog WATSON-CRICK E DG 9 B N1 DG 9 1_555 F DC 6 C N3 DC 6 1_555 hydrog WATSON-CRICK E DG 9 B N2 DG 9 1_555 F DC 6 C O2 DC 6 1_555 hydrog WATSON-CRICK E DG 9 B O6 DG 9 1_555 F DC 6 C N4 DC 6 1_555 hydrog WATSON-CRICK E DG 10 B N1 DG 10 1_555 F DC 5 C N3 DC 5 1_555 hydrog WATSON-CRICK E DG 10 B N2 DG 10 1_555 F DC 5 C O2 DC 5 1_555 hydrog WATSON-CRICK E DG 10 B O6 DG 10 1_555 F DC 5 C N4 DC 5 1_555 hydrog WATSON-CRICK E DC 11 B N3 DC 11 1_555 F DG 4 C N1 DG 4 1_555 hydrog WATSON-CRICK E DC 11 B N4 DC 11 1_555 F DG 4 C O6 DG 4 1_555 hydrog WATSON-CRICK E DC 11 B O2 DC 11 1_555 F DG 4 C N2 DG 4 1_555 hydrog WATSON-CRICK E DT 12 B N3 DT 12 1_555 F DA 3 C N1 DA 3 1_555 hydrog WATSON-CRICK E DT 12 B O4 DT 12 1_555 F DA 3 C N6 DA 3 1_555 hydrog TYPE_8_PAIR E DA 13 B N1 DA 13 1_555 F DG 1 C N1 DG 1 1_555 hydrog TYPE_8_PAIR E DA 13 B N6 DA 13 1_555 F DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK E DA 13 B N1 DA 13 1_555 F DT 2 C N3 DT 2 1_555 hydrog WATSON-CRICK E DA 13 B N6 DA 13 1_555 F DT 2 C O4 DT 2 1_555 hydrog WATSON-CRICK E DC 14 B N3 DC 14 1_555 F DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK E DC 14 B N4 DC 14 1_555 F DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK E DC 14 B O2 DC 14 1_555 F DG 1 C N2 DG 1 1_555 GENE REGULATION/DNA Deaminase, GENE REGULATION, GENE REGULATION-DNA complex A PHE 1985 A PHE 35 1 A PRO 1986 A PRO 36 10.65 9PW1 PDB 1 1 9PW1 9PW1 PDB 2 1 9PW1 9PW1 PDB 3 1 9PW1 1951 2054 9PW1 1951 2054 9PW1 A 1 1 104 1 14 9PW1 1 14 9PW1 E 2 1 14 1 14 9PW1 1 14 9PW1 F 3 1 14 5 anti-parallel anti-parallel parallel anti-parallel A VAL 1965 A VAL 15 A VAL 1972 A VAL 22 A LYS 1953 A LYS 3 A THR 1959 A THR 9 A THR 2009 A THR 59 A GLU 2013 A GLU 63 A LYS 2036 A LYS 86 A GLU 2043 A GLU 93 A ASP 2046 A ASP 96 A GLU 2053 A GLU 103 97 I 4 2 2