0.019668 0.000000 0.000000 0.000000 0.019067 0.000000 0.000000 0.000000 0.014698 0.00000 0.00000 0.00000 Shi, K. Kurahashi, K. Aihara, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 50.843 52.448 68.035 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 Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer 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 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 CL N 75 N N N 76 R C N 77 N C N 78 N O N 79 N C N 80 N S N 81 N O 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 H N 89 N O N 90 N P N 91 N O N 92 N O N 93 N O N 94 N C N 95 R C N 96 N O N 97 S C N 98 N O N 99 N C N 100 R C N 101 N N N 102 N C N 103 N O N 104 N N N 105 N C N 106 N N N 107 N C N 108 N C N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H 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 C N 124 N O N 125 N C N 126 N O N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N N N 134 S C N 135 N C N 136 N O N 137 N C N 138 N C N 139 N C N 140 N O N 141 N N N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N N N 154 S C N 155 N C N 156 N O N 157 N C N 158 N C N 159 N C N 160 N O N 161 N O N 162 N O 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 H N 170 N H N 171 N H N 172 N N N 173 N C N 174 N C N 175 N O N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N N N 183 S C N 184 N C N 185 N O N 186 N C Y 187 N C Y 188 N N Y 189 N C Y 190 N C Y 191 N N N 192 N O 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 O N 204 N H N 205 N H N 206 N N N 207 S C N 208 N C N 209 N O N 210 S C N 211 N C N 212 N C N 213 N C 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 N N 229 S C N 230 N C N 231 N O N 232 N C N 233 N C N 234 N C N 235 N C N 236 N O N 237 N H N 238 N H 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 N 255 N C N 256 N C N 257 N C N 258 N N N 259 N O N 260 N H N 261 N H 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 H N 274 N H N 275 N N N 276 S C N 277 N C N 278 N O N 279 N C N 280 N C N 281 N S N 282 N C N 283 N O 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 H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N N N 296 S C N 297 N C N 298 N O N 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N C Y 305 N C N 306 N O 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 H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N N N 319 S C N 320 N C N 321 N O N 322 N C N 323 N C N 324 N C N 325 N O 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 H N 334 N H N 335 N N N 336 S C N 337 N C N 338 N O N 339 N C N 340 N O 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 N N 350 S C N 351 N C N 352 N O N 353 R C N 354 N O N 355 N C N 356 N O N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N N N 367 S C N 368 N C N 369 N O N 370 N C Y 371 N C Y 372 N C Y 373 N C Y 374 N N Y 375 N C Y 376 N C Y 377 N C Y 378 N C Y 379 N C N 380 N O 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 391 N H N 392 N H N 393 N N N 394 S C N 395 N C N 396 N O N 397 N C Y 398 N C Y 399 N C Y 400 N C Y 401 N C Y 402 N C Y 403 N C N 404 N O N 405 N O N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N N N 418 S C N 419 N C N 420 N O N 421 N C N 422 N C N 423 N C N 424 N O N 425 N H N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N ZN 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 doub 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 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 doub N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing 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 doub 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 doub 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 sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N doub 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 doub 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 Y 184 N sing Y 185 N doub Y 186 N doub N 187 N sing Y 188 N sing N 189 N sing Y 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 doub 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 doub 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 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 sing 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 sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N doub 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 sing N 284 N sing N 285 N sing N 286 N sing N 287 N doub N 288 N sing N 289 N sing N 290 N sing N 291 N sing Y 292 N doub Y 293 N sing Y 294 N sing N 295 N sing Y 296 N doub N 297 N sing Y 298 N doub N 299 N sing Y 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 doub 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 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 doub 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 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 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 sing N 356 N doub N 357 N sing N 358 N sing N 359 N sing N 360 N sing Y 361 N doub Y 362 N sing Y 363 N sing N 364 N sing Y 365 N doub Y 366 N sing Y 367 N sing N 368 N sing Y 369 N sing Y 370 N doub N 371 N sing Y 372 N doub N 373 N sing Y 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 N 383 N sing N 384 N doub N 385 N sing N 386 N sing N 387 N sing N 388 N sing Y 389 N doub Y 390 N sing Y 391 N sing N 392 N sing Y 393 N doub N 394 N sing Y 395 N doub N 396 N sing Y 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N doub N 409 N sing N 410 N sing N 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 US J.Biol.Chem. JBCHA3 0071 1083-351X 290 28120 28130 10.1074/jbc.M115.679951 26416889 Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. 2015 10.2210/pdb5cqh/pdb pdb_00005cqh 100 1 PIXEL 2014-11-24 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 0.979 1.0 24-ID-C APS 0.979 SYNCHROTRON APS BEAMLINE 24-ID-C 21978.963 DNA dC-dU-editing enzyme APOBEC-3B 3.5.4.- UNP Residues 187-378 1 man polymer 65.409 ZINC ION 1 syn non-polymer 307.197 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE 1 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 62.068 1,2-ETHANEDIOL 4 syn non-polymer 18.015 water 185 nat water A3B,Phorbolin-1-related protein,Phorbolin-2/3 no no MEILRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIY RVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQG CPFQPWDGLEEHSQALSGRLRAILQL MEILRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIY RVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQG CPFQPWDGLEEHSQALSGRLRAILQL 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 Human sample 1 186 APOBEC3B 9606 Homo sapiens 562 Escherichia coli Biological sequence 2.06 40.40 VAPOR DIFFUSION, HANGING DROP PEG 3350, MES-NaOH 293 pdbx_audit_support pdbx_struct_oper_list pdbx_audit_support chem_comp_atom chem_comp_bond database_2 repository Initial release Database references Database references Data collection Author supporting evidence Derived calculations Author supporting evidence Data collection Database references 1 0 2015-10-07 1 1 2015-10-14 1 2 2015-12-02 1 3 2016-07-20 1 4 2017-09-27 1 5 2019-12-25 1 6 2024-03-06 _pdbx_audit_support.funding_organization _pdbx_struct_oper_list.symmetry_operation _pdbx_audit_support.funding_organization _database_2.pdbx_DOI _database_2.pdbx_database_accession United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) N RCSB Y RCSB 2015-07-21 REL REL 1 A O HOH 685 6.50 ZN ZINC ION DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE CL CHLORIDE ION EDO 1,2-ETHANEDIOL HOH water ZN 2 2 ZN ZN 401 A Cd 1 3 DC DC 402 A CL 1 4 CL CL 403 A EDO 1 5 EDO EDO 404 A EDO 2 5 EDO EDO 405 A EDO 3 5 EDO EDO 406 A EDO 4 5 EDO EDO 407 A HOH 107 6 HOH HOH 501 A HOH 171 6 HOH HOH 502 A HOH 88 6 HOH HOH 503 A HOH 102 6 HOH HOH 504 A HOH 51 6 HOH HOH 505 A HOH 101 6 HOH HOH 506 A HOH 157 6 HOH HOH 507 A HOH 94 6 HOH HOH 508 A HOH 160 6 HOH HOH 509 A HOH 72 6 HOH HOH 510 A HOH 152 6 HOH HOH 511 A HOH 96 6 HOH HOH 512 A HOH 4 6 HOH HOH 513 A HOH 177 6 HOH HOH 514 A HOH 52 6 HOH HOH 515 A HOH 116 6 HOH HOH 516 A HOH 105 6 HOH HOH 517 A HOH 8 6 HOH HOH 518 A HOH 142 6 HOH HOH 519 A HOH 78 6 HOH HOH 520 A HOH 80 6 HOH HOH 521 A HOH 6 6 HOH HOH 522 A HOH 64 6 HOH HOH 523 A HOH 54 6 HOH HOH 524 A HOH 181 6 HOH HOH 525 A HOH 55 6 HOH HOH 526 A HOH 111 6 HOH HOH 527 A HOH 81 6 HOH HOH 528 A HOH 91 6 HOH HOH 529 A HOH 148 6 HOH HOH 530 A HOH 16 6 HOH HOH 531 A HOH 103 6 HOH HOH 532 A HOH 132 6 HOH HOH 533 A HOH 37 6 HOH HOH 534 A HOH 67 6 HOH HOH 535 A HOH 32 6 HOH HOH 536 A HOH 144 6 HOH HOH 537 A HOH 175 6 HOH HOH 538 A HOH 70 6 HOH HOH 539 A HOH 2 6 HOH HOH 540 A HOH 166 6 HOH HOH 541 A HOH 3 6 HOH HOH 542 A HOH 124 6 HOH HOH 543 A HOH 7 6 HOH HOH 544 A HOH 9 6 HOH HOH 545 A HOH 34 6 HOH HOH 546 A HOH 140 6 HOH HOH 547 A HOH 110 6 HOH HOH 548 A HOH 104 6 HOH HOH 549 A HOH 93 6 HOH HOH 550 A HOH 87 6 HOH HOH 551 A HOH 29 6 HOH HOH 552 A HOH 66 6 HOH HOH 553 A HOH 176 6 HOH HOH 554 A HOH 59 6 HOH HOH 555 A HOH 60 6 HOH HOH 556 A HOH 85 6 HOH HOH 557 A HOH 69 6 HOH HOH 558 A HOH 47 6 HOH HOH 559 A HOH 39 6 HOH HOH 560 A HOH 49 6 HOH HOH 561 A HOH 40 6 HOH HOH 562 A HOH 28 6 HOH HOH 563 A HOH 23 6 HOH HOH 564 A HOH 82 6 HOH HOH 565 A HOH 27 6 HOH HOH 566 A HOH 35 6 HOH HOH 567 A HOH 45 6 HOH HOH 568 A HOH 100 6 HOH HOH 569 A HOH 120 6 HOH HOH 570 A HOH 12 6 HOH HOH 571 A HOH 109 6 HOH HOH 572 A HOH 99 6 HOH HOH 573 A HOH 61 6 HOH HOH 574 A HOH 138 6 HOH HOH 575 A HOH 76 6 HOH HOH 576 A HOH 10 6 HOH HOH 577 A HOH 46 6 HOH HOH 578 A HOH 167 6 HOH HOH 579 A HOH 18 6 HOH HOH 580 A HOH 155 6 HOH HOH 581 A HOH 178 6 HOH HOH 582 A HOH 57 6 HOH HOH 583 A HOH 89 6 HOH HOH 584 A HOH 92 6 HOH HOH 585 A HOH 1 6 HOH HOH 586 A HOH 153 6 HOH HOH 587 A HOH 21 6 HOH HOH 588 A HOH 139 6 HOH HOH 589 A HOH 128 6 HOH HOH 590 A HOH 22 6 HOH HOH 591 A HOH 95 6 HOH HOH 592 A HOH 56 6 HOH HOH 593 A HOH 14 6 HOH HOH 594 A HOH 30 6 HOH HOH 595 A HOH 135 6 HOH HOH 596 A HOH 63 6 HOH HOH 597 A HOH 154 6 HOH HOH 598 A HOH 15 6 HOH HOH 599 A HOH 149 6 HOH HOH 600 A HOH 73 6 HOH HOH 601 A HOH 44 6 HOH HOH 602 A HOH 5 6 HOH HOH 603 A HOH 136 6 HOH HOH 604 A HOH 163 6 HOH HOH 605 A HOH 68 6 HOH HOH 606 A HOH 41 6 HOH HOH 607 A HOH 24 6 HOH HOH 608 A HOH 36 6 HOH HOH 609 A HOH 79 6 HOH HOH 610 A HOH 86 6 HOH HOH 611 A HOH 71 6 HOH HOH 612 A HOH 113 6 HOH HOH 613 A HOH 65 6 HOH HOH 614 A HOH 74 6 HOH HOH 615 A HOH 77 6 HOH HOH 616 A HOH 13 6 HOH HOH 617 A HOH 162 6 HOH HOH 618 A HOH 106 6 HOH HOH 619 A HOH 117 6 HOH HOH 620 A HOH 169 6 HOH HOH 621 A HOH 126 6 HOH HOH 622 A HOH 118 6 HOH HOH 623 A HOH 31 6 HOH HOH 624 A HOH 42 6 HOH HOH 625 A HOH 26 6 HOH HOH 626 A HOH 17 6 HOH HOH 627 A HOH 50 6 HOH HOH 628 A HOH 25 6 HOH HOH 629 A HOH 137 6 HOH HOH 630 A HOH 11 6 HOH HOH 631 A HOH 62 6 HOH HOH 632 A HOH 114 6 HOH HOH 633 A HOH 121 6 HOH HOH 634 A HOH 183 6 HOH HOH 635 A HOH 134 6 HOH HOH 636 A HOH 19 6 HOH HOH 637 A HOH 151 6 HOH HOH 638 A HOH 38 6 HOH HOH 639 A HOH 98 6 HOH HOH 640 A HOH 119 6 HOH HOH 641 A HOH 58 6 HOH HOH 642 A HOH 43 6 HOH HOH 643 A HOH 48 6 HOH HOH 644 A HOH 156 6 HOH HOH 645 A HOH 20 6 HOH HOH 646 A HOH 141 6 HOH HOH 647 A HOH 145 6 HOH HOH 648 A HOH 168 6 HOH HOH 649 A HOH 115 6 HOH HOH 650 A HOH 184 6 HOH HOH 651 A HOH 164 6 HOH HOH 652 A HOH 170 6 HOH HOH 653 A HOH 123 6 HOH HOH 654 A HOH 90 6 HOH HOH 655 A HOH 165 6 HOH HOH 656 A HOH 158 6 HOH HOH 657 A HOH 179 6 HOH HOH 658 A HOH 97 6 HOH HOH 659 A HOH 112 6 HOH HOH 660 A HOH 83 6 HOH HOH 661 A HOH 143 6 HOH HOH 662 A HOH 147 6 HOH HOH 663 A HOH 159 6 HOH HOH 664 A HOH 150 6 HOH HOH 665 A HOH 122 6 HOH HOH 666 A HOH 75 6 HOH HOH 667 A HOH 127 6 HOH HOH 668 A HOH 33 6 HOH HOH 669 A HOH 180 6 HOH HOH 670 A HOH 84 6 HOH HOH 671 A HOH 182 6 HOH HOH 672 A HOH 53 6 HOH HOH 673 A HOH 174 6 HOH HOH 674 A HOH 131 6 HOH HOH 675 A HOH 146 6 HOH HOH 676 A HOH 108 6 HOH HOH 677 A HOH 172 6 HOH HOH 678 A HOH 130 6 HOH HOH 679 A HOH 173 6 HOH HOH 680 A HOH 125 6 HOH HOH 681 A HOH 161 6 HOH HOH 682 A HOH 185 6 HOH HOH 683 A HOH 129 6 HOH HOH 684 A HOH 133 6 HOH HOH 685 A n 1 186 A n 2 187 A n 3 188 A ALA 189 n 4 LEU 189 A ARG 190 n 5 ARG 190 A TYR 191 n 6 TYR 191 A LEU 192 n 7 LEU 192 A MET 193 n 8 MET 193 A ASP 194 n 9 ASP 194 A PRO 195 n 10 PRO 195 A ASP 196 n 11 ASP 196 A THR 197 n 12 THR 197 A PHE 198 n 13 PHE 198 A THR 199 n 14 THR 199 A SER 200 n 15 SER 200 A ASN 201 n 16 ASN 201 A PHE 202 n 17 PHE 202 A ASN 203 n 18 ASN 203 A ASN 204 n 19 ASN 204 A ASP 205 n 20 ASP 205 A PRO 206 n 21 PRO 206 A LEU 207 n 22 LEU 207 A VAL 208 n 23 VAL 208 A LEU 209 n 24 LEU 209 A ARG 210 n 25 ARG 210 A ARG 211 n 26 ARG 211 A ARG 212 n 27 ARG 212 A GLN 213 n 28 GLN 213 A THR 214 n 29 THR 214 A TYR 215 n 30 TYR 215 A LEU 216 n 31 LEU 216 A CYS 217 n 32 CYS 217 A TYR 218 n 33 TYR 218 A GLU 219 n 34 GLU 219 A VAL 220 n 35 VAL 220 A GLU 221 n 36 GLU 221 A ARG 222 n 37 ARG 222 A LEU 223 n 38 LEU 223 A ASP 224 n 39 ASP 224 A ASN 225 n 40 ASN 225 A GLY 226 n 41 GLY 226 A THR 227 n 42 THR 227 A SER 228 n 43 SER 228 A VAL 229 n 44 VAL 229 A LYS 230 n 45 LYS 230 A MET 231 n 46 MET 231 A ASP 232 n 47 ASP 232 A GLN 233 n 48 GLN 233 A HIS 234 n 49 HIS 234 A MET 235 n 50 MET 235 A GLY 236 n 51 GLY 236 A PHE 237 n 52 PHE 237 A LEU 238 n 53 LEU 238 A CYS 239 n 54 CYS 239 A ASN 240 n 55 ASN 240 A GLU 241 n 56 GLU 241 A SER 250 n 57 SER 250 A GLY 251 n 58 GLY 251 A ARG 252 n 59 ARG 252 A HIS 253 n 60 HIS 253 A ALA 254 n 61 ALA 254 A GLU 255 n 62 GLU 255 A LEU 256 n 63 LEU 256 A ARG 257 n 64 ARG 257 A PHE 258 n 65 PHE 258 A LEU 259 n 66 LEU 259 A ASP 260 n 67 ASP 260 A LEU 261 n 68 LEU 261 A VAL 262 n 69 VAL 262 A PRO 263 n 70 PRO 263 A SER 264 n 71 SER 264 A LEU 265 n 72 LEU 265 A GLN 266 n 73 GLN 266 A LEU 267 n 74 LEU 267 A ASP 268 n 75 ASP 268 A PRO 269 n 76 PRO 269 A ALA 270 n 77 ALA 270 A GLN 271 n 78 GLN 271 A ILE 272 n 79 ILE 272 A TYR 273 n 80 TYR 273 A ARG 274 n 81 ARG 274 A VAL 275 n 82 VAL 275 A THR 276 n 83 THR 276 A TRP 277 n 84 TRP 277 A PHE 278 n 85 PHE 278 A ILE 279 n 86 ILE 279 A SER 280 n 87 SER 280 A TRP 281 n 88 TRP 281 A SER 282 n 89 SER 282 A PRO 283 n 90 PRO 283 A CYS 284 n 91 CYS 284 A PHE 285 n 92 PHE 285 A SER 286 n 93 SER 286 A TRP 287 n 94 TRP 287 A GLY 288 n 95 GLY 288 A CYS 289 n 96 CYS 289 A ALA 290 n 97 ALA 290 A GLY 291 n 98 GLY 291 A GLU 292 n 99 GLU 292 A VAL 293 n 100 VAL 293 A ARG 294 n 101 ARG 294 A ALA 295 n 102 ALA 295 A PHE 296 n 103 PHE 296 A LEU 297 n 104 LEU 297 A GLN 298 n 105 GLN 298 A GLU 299 n 106 GLU 299 A ASN 300 n 107 ASN 300 A THR 301 n 108 THR 301 A HIS 302 n 109 HIS 302 A VAL 303 n 110 VAL 303 A ARG 304 n 111 ARG 304 A LEU 305 n 112 LEU 305 A ARG 306 n 113 ARG 306 A ILE 307 n 114 ILE 307 A LYS 308 n 115 LYS 308 A ALA 309 n 116 ALA 309 A ALA 310 n 117 ALA 310 A ARG 311 n 118 ARG 311 A ILE 312 n 119 ILE 312 A TYR 313 n 120 TYR 313 A ASP 314 n 121 ASP 314 A TYR 315 n 122 TYR 315 A ASP 316 n 123 ASP 316 A PRO 317 n 124 PRO 317 A LEU 318 n 125 LEU 318 A TYR 319 n 126 TYR 319 A LYS 320 n 127 LYS 320 A GLU 321 n 128 GLU 321 A ALA 322 n 129 ALA 322 A LEU 323 n 130 LEU 323 A GLN 324 n 131 GLN 324 A MET 325 n 132 MET 325 A LEU 326 n 133 LEU 326 A ARG 327 n 134 ARG 327 A ASP 328 n 135 ASP 328 A ALA 329 n 136 ALA 329 A GLY 330 n 137 GLY 330 A ALA 331 n 138 ALA 331 A GLN 332 n 139 GLN 332 A VAL 333 n 140 VAL 333 A SER 334 n 141 SER 334 A ILE 335 n 142 ILE 335 A MET 336 n 143 MET 336 A THR 337 n 144 THR 337 A TYR 338 n 145 TYR 338 A ASP 339 n 146 ASP 339 A GLU 340 n 147 GLU 340 A PHE 341 n 148 PHE 341 A GLU 342 n 149 GLU 342 A TYR 343 n 150 TYR 343 A CYS 344 n 151 CYS 344 A TRP 345 n 152 TRP 345 A ASP 346 n 153 ASP 346 A THR 347 n 154 THR 347 A PHE 348 n 155 PHE 348 A VAL 349 n 156 VAL 349 A TYR 350 n 157 TYR 350 A ARG 351 n 158 ARG 351 A GLN 352 n 159 GLN 352 A GLY 353 n 160 GLY 353 A CYS 354 n 161 CYS 354 A PRO 355 n 162 PRO 355 A PHE 356 n 163 PHE 356 A GLN 357 n 164 GLN 357 A PRO 358 n 165 PRO 358 A TRP 359 n 166 TRP 359 A ASP 360 n 167 ASP 360 A GLY 361 n 168 GLY 361 A LEU 362 n 169 LEU 362 A GLU 363 n 170 GLU 363 A GLU 364 n 171 GLU 364 A HIS 365 n 172 HIS 365 A SER 366 n 173 SER 366 A GLN 367 n 174 GLN 367 A ALA 368 n 175 ALA 368 A LEU 369 n 176 LEU 369 A SER 370 n 177 SER 370 A GLY 371 n 178 GLY 371 A ARG 372 n 179 ARG 372 A LEU 373 n 180 LEU 373 A ARG 374 n 181 ARG 374 A ALA 375 n 182 ALA 375 A ILE 376 n 183 ILE 376 A LEU 377 n 184 LEU 377 A GLN 378 n 185 GLN 378 A LEU 379 n 186 LEU 379 A 6.9200 2.1456 -1.4288 5.8884 -2.5237 6.0428 -0.0060 0.4256 0.0791 -0.3117 0.1543 -0.2504 0.1061 0.0803 -0.0753 0.1033 0.0250 0.0046 0.1739 -0.0270 0.0932 refined -0.6908 -11.9846 -4.1927 X-RAY DIFFRACTION 2.1178 0.2958 -0.0800 2.5190 -0.1907 1.9461 0.0602 -0.0475 -0.0769 -0.0283 -0.0649 -0.0299 -0.0207 0.0372 -0.0169 0.0951 0.0161 -0.0023 0.1157 -0.0067 0.0593 refined -5.6082 -10.6088 4.6285 X-RAY DIFFRACTION 5.4260 -4.8021 2.3781 6.2463 -1.5943 2.5519 0.0015 0.2150 0.3324 -0.3552 -0.1196 0.2546 -0.2948 -0.2468 0.0589 0.2142 0.0378 -0.0148 0.1950 0.0313 0.1854 refined -10.9968 1.9111 -2.8619 X-RAY DIFFRACTION 1.0196 0.1634 0.0812 1.3306 0.1888 1.9046 0.0150 -0.0369 0.1092 0.0961 -0.0236 0.0022 -0.1431 -0.0236 0.0183 0.0839 0.0050 0.0014 0.1142 0.0006 0.1050 refined -8.5535 -4.9282 9.8818 X-RAY DIFFRACTION 2.0261 1.2827 -0.8512 1.9023 -1.1335 4.6096 -0.0429 0.1694 -0.2541 -0.1297 0.0350 -0.0394 0.3527 -0.1637 -0.0053 0.0627 0.0067 -0.0487 0.1191 -0.0140 0.1111 refined -12.1216 -19.1868 2.4583 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resid 189 through 202 ) X-RAY DIFFRACTION 2 chain 'A' and (resid 203 through 224 ) X-RAY DIFFRACTION 3 chain 'A' and (resid 225 through 239 ) X-RAY DIFFRACTION 4 chain 'A' and (resid 240 through 348 ) X-RAY DIFFRACTION 5 chain 'A' and (resid 349 through 379 ) author_and_software_defined_assembly PISA 1 monomeric A HIS 253 A ND1 HIS 60 1_555 A ZN 401 B ZN ZN 1_555 A CYS 284 A SG CYS 91 1_555 114.4 A HIS 253 A ND1 HIS 60 1_555 A ZN 401 B ZN ZN 1_555 A CYS 289 A SG CYS 96 1_555 113.0 A CYS 284 A SG CYS 91 1_555 A ZN 401 B ZN ZN 1_555 A CYS 289 A SG CYS 96 1_555 114.0 A HIS 253 A ND1 HIS 60 1_555 A ZN 401 B ZN ZN 1_555 A EDO 405 F O2 EDO 1_555 100.7 A CYS 284 A SG CYS 91 1_555 A ZN 401 B ZN ZN 1_555 A EDO 405 F O2 EDO 1_555 107.1 A CYS 289 A SG CYS 96 1_555 A ZN 401 B ZN ZN 1_555 A EDO 405 F O2 EDO 1_555 106.3 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 O THR 227 A O THR 42 A N ASP 224 A N ASP 39 A N TYR 218 A N TYR 33 A O GLY 236 A O GLY 51 A O THR 227 A O THR 42 A N ASP 224 A N ASP 39 A N GLU 219 A N GLU 34 A O THR 276 A O THR 83 A N TRP 277 A N TRP 84 A O LYS 308 A O LYS 115 A N ILE 307 A N ILE 114 A O GLN 332 A O GLN 139 1 A CG LEU 189 A CG LEU 4 1 Y 1 A CD1 LEU 189 A CD1 LEU 4 1 Y 1 A CD2 LEU 189 A CD2 LEU 4 1 Y 1 A MET 186 A MET 1 1 Y 1 A GLU 187 A GLU 2 1 Y 1 A ILE 188 A ILE 3 1 Y 1 A A O O HOH HOH 533 589 1.98 1 A A OD2 O ASP HOH 232 501 2.11 1 A A O O HOH HOH 556 668 2.12 1 A A O O HOH HOH 589 662 2.16 1 -3.17 0.50 120.30 117.13 A A A NE CZ NH1 ARG ARG ARG 190 190 190 N 1 A A O O HOH HOH 621 658 2.09 1_555 3_545 1 A ARG 210 -151.86 31.40 1 A ASN 225 39.90 72.06 0.1859 0.1523 0.1541 1.730 40.7 998 19544 5.11 99.78 0.19 Random selection 1 FREE R-VALUE 1.35 18.17 0.90 1.11 ML FLAT BULK SOLVENT MODEL 1.730 40.7 185 1739 38 0 1516 0.018 1614 1.652 2189 17.201 948 0.100 225 0.010 285 0.2940 0.2306 1.8213 137 2615 100.00 0.2268 0.1781 1.9354 148 2581 100.00 0.1998 0.1584 2.0848 121 2655 100.00 0.1901 0.1444 2.2946 160 2603 100.00 0.1815 0.1440 2.6266 166 2625 100.00 0.1777 0.1494 3.3090 126 2686 100.00 0.1614 0.1407 40.7383 140 2781 99.00 1.73 40.7 5CQH 19558 1 17.3 4.7 100 refinement PHENIX (dev_2067: ???) data reduction HKL-2000 data scaling SCALEPACK phasing PHASER Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N 5 N N 6 N N A ASP 194 A ASP 9 HELX_P A ASN 203 A ASN 18 1 AA1 10 A ASP 232 A ASP 47 HELX_P A MET 235 A MET 50 5 AA2 4 A HIS 253 A HIS 60 HELX_P A GLN 266 A GLN 73 1 AA3 14 A GLY 288 A GLY 95 HELX_P A ASN 300 A ASN 107 1 AA4 13 A LEU 318 A LEU 125 HELX_P A ALA 329 A ALA 136 1 AA5 12 A THR 337 A THR 144 HELX_P A VAL 349 A VAL 156 1 AA6 13 A GLY 361 A GLY 168 HELX_P A GLN 378 A GLN 185 1 AA7 18 metalc 2.001 A HIS 253 A ND1 HIS 60 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.295 A CYS 284 A SG CYS 91 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.267 A CYS 289 A SG CYS 96 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.067 A ZN 401 B ZN ZN 1_555 A EDO 405 F O2 EDO 1_555 HYDROLASE APOBEC, deaminase, HYDROLASE ABC3B_HUMAN UNP 1 187 Q9UH17 EILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQ LDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWD TFVYRQGCPFQPWDGLEEHSQALSGRLRAILQ 187 378 5CQH 187 378 Q9UH17 A 1 2 185 1 initiating methionine MET 186 5CQH A Q9UH17 UNP 1 1 PHE conflict SER 200 5CQH A Q9UH17 UNP 200 15 1 TRP conflict SER 228 5CQH A Q9UH17 UNP 228 43 1 LEU conflict LYS 230 5CQH A Q9UH17 UNP 230 45 1 ALA deletion 5CQH A Q9UH17 UNP 242 1 LYS deletion 5CQH A Q9UH17 UNP 243 1 ASN deletion 5CQH A Q9UH17 UNP 244 1 LEU deletion 5CQH A Q9UH17 UNP 245 1 LEU deletion 5CQH A Q9UH17 UNP 246 1 CYS deletion 5CQH A Q9UH17 UNP 247 1 GLY deletion 5CQH A Q9UH17 UNP 248 1 PHE deletion 5CQH A Q9UH17 UNP 249 1 TYR conflict SER 250 5CQH A Q9UH17 UNP 250 57 1 PHE conflict LYS 308 5CQH A Q9UH17 UNP 308 115 1 expression tag LEU 379 5CQH A Q9UH17 UNP 186 3 5 anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel A THR 227 A THR 42 A LYS 230 A LYS 45 A TYR 215 A TYR 30 A ASP 224 A ASP 39 A GLY 236 A GLY 51 A CYS 239 A CYS 54 A THR 227 A THR 42 A LYS 230 A LYS 45 A TYR 215 A TYR 30 A ASP 224 A ASP 39 A ILE 272 A ILE 79 A ILE 279 A ILE 86 A VAL 303 A VAL 110 A ALA 309 A ALA 116 A GLN 332 A GLN 139 A ILE 335 A ILE 142 binding site for residue ZN A 401 A ZN 401 Software 4 binding site for residue DC A 402 A DC 402 Software 13 binding site for residue CL A 403 A CL 403 Software 3 binding site for residue EDO A 404 A EDO 404 Software 6 binding site for residue EDO A 405 A EDO 405 Software 7 binding site for residue EDO A 406 A EDO 406 Software 6 binding site for residue EDO A 407 A EDO 407 Software 6 A HIS 253 A HIS 60 4 1_555 A CYS 284 A CYS 91 4 1_555 A CYS 289 A CYS 96 4 1_555 A EDO 405 F EDO 4 1_555 A ARG 252 A ARG 59 13 3_545 A ASP 260 A ASP 67 13 3_545 A ASP 314 A ASP 121 13 1_555 A TYR 319 A TYR 126 13 1_555 A LYS 320 A LYS 127 13 1_555 A ARG 372 A ARG 179 13 1_555 A HOH 504 I HOH 13 1_555 A HOH 549 I HOH 13 1_555 A HOH 554 I HOH 13 1_555 A HOH 559 I HOH 13 1_555 A HOH 598 I HOH 13 1_555 A HOH 616 I HOH 13 1_555 A HOH 620 I HOH 13 1_555 A ILE 335 A ILE 142 3 1_555 A SER 370 A SER 177 3 1_555 A ARG 374 A ARG 181 3 1_555 A PRO 206 A PRO 21 6 3_555 A ARG 252 A ARG 59 6 1_555 A TRP 287 A TRP 94 6 1_555 A GLU 292 A GLU 99 6 1_555 A HOH 510 I HOH 6 1_555 A HOH 580 I HOH 6 1_555 A THR 214 A THR 29 7 1_555 A HIS 253 A HIS 60 7 1_555 A GLU 255 A GLU 62 7 1_555 A SER 282 A SER 89 7 1_555 A CYS 284 A CYS 91 7 1_555 A CYS 289 A CYS 96 7 1_555 A ZN 401 B ZN 7 1_555 A CYS 239 A CYS 54 6 1_555 A THR 337 A THR 144 6 4_545 A TYR 338 A TYR 145 6 4_545 A ASP 339 A ASP 146 6 4_545 A HOH 560 I HOH 6 1_555 A HOH 562 I HOH 6 1_555 A ASP 339 A ASP 146 6 1_555 A GLU 340 A GLU 147 6 1_555 A TYR 343 A TYR 150 6 1_555 A HOH 516 I HOH 6 1_555 A HOH 622 I HOH 6 1_555 A HOH 640 I HOH 6 1_555 19 P 21 21 21