0.024640 0.000000 0.000000 0.000000 0.014743 0.000000 0.000000 0.000000 0.008838 0.00000 0.00000 0.00000 Umitsu, M. Nishimasu, H. Ishitani, R. Nureki, O. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 40.584 67.827 113.150 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 C15 H22 N6 O5 S 398.437 S-ADENOSYLMETHIONINE non-polymer 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 O N 295 N C N 296 N C N 297 S S N 298 N C N 299 N C N 300 S C N 301 N O N 302 S C N 303 N O N 304 R C N 305 N O N 306 R C Y 307 N N Y 308 N C Y 309 N N Y 310 N C Y 311 N C N 312 N N Y 313 N N Y 314 N C Y 315 N N Y 316 N C N 317 N H N 318 N H N 319 N H 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 H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N N N 340 S C N 341 N C N 342 N O N 343 N C N 344 N O N 345 N O 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 N N 354 S C N 355 N C N 356 N O N 357 R C N 358 N O N 359 N C 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 N N 371 S C N 372 N C N 373 N O N 374 N C Y 375 N C Y 376 N C Y 377 N C Y 378 N N Y 379 N C Y 380 N C Y 381 N C Y 382 N C Y 383 N C N 384 N O 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 H N 394 N H N 395 N H N 396 N H N 397 N N N 398 S C N 399 N C N 400 N O N 401 N C Y 402 N C Y 403 N C Y 404 N C Y 405 N C Y 406 N C Y 407 N C N 408 N O N 409 N O 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 H N 418 N H N 419 N H N 420 N H N 421 N N N 422 S C N 423 N C N 424 N O N 425 N C N 426 N C N 427 N C N 428 N O 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 H N 437 N H N 438 N H N 439 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 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 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 Y 313 N sing Y 314 N sing Y 315 N doub N 316 N sing Y 317 N sing Y 318 N sing Y 319 N doub N 320 N sing Y 321 N doub N 322 N sing N 323 N sing Y 324 N sing Y 325 N doub N 326 N sing Y 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 doub 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 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 doub N 364 N sing N 365 N sing N 366 N sing N 367 N sing Y 368 N doub Y 369 N sing Y 370 N sing N 371 N sing Y 372 N doub Y 373 N sing Y 374 N sing N 375 N sing Y 376 N sing Y 377 N doub N 378 N sing Y 379 N doub N 380 N sing Y 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 doub N 392 N sing N 393 N sing N 394 N sing N 395 N sing Y 396 N doub Y 397 N sing Y 398 N sing N 399 N sing Y 400 N doub N 401 N sing Y 402 N doub N 403 N sing Y 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing 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 doub N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 106 15616 15621 10.1073/pnas.0905270106 19717466 Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2 2009 10.2210/pdb3a27/pdb pdb_00003a27 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2008-10-19 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 1.00 1.0 BL41XU SPring-8 1.00 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 31912.244 Uncharacterized protein MJ1557 1 man polymer 398.437 S-ADENOSYLMETHIONINE 1 syn non-polymer 18.015 water 79 nat water TYW2 no no MGSSHHHHHHSSGLEVLFQGPLHMGIKYQKIGDVVIVKKELSEDEIREIVKRTKCKAILLYTTQITGEFRTPHVKILYGK ETETIHKEYGCLFKLDVAKIMWSQGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLC ENIKLNKLNNVIPILADNRDVELKDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHETVAEKIMYERPIERLKFYAEK NGYKLIDYEVRKIKKYAPGVWHVVVDAKFERI MGSSHHHHHHSSGLEVLFQGPLHMGIKYQKIGDVVIVKKELSEDEIREIVKRTKCKAILLYTTQITGEFRTPHVKILYGK ETETIHKEYGCLFKLDVAKIMWSQGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLC ENIKLNKLNNVIPILADNRDVELKDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHETVAEKIMYERPIERLKFYAEK NGYKLIDYEVRKIKKYAPGVWHVVVDAKFERI 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 Methanococcus jannaschii sample MJ1557 2190 Methanocaldococcus jannaschii 562 Escherichia coli BL21 plasmid pET28a 1 2.44 49.59 VAPOR DIFFUSION, HANGING DROP 6.5 0.1M MES, 0.1M ammonium sulfate, 15% PEG5000, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2009-09-15 1 1 2011-07-13 1 2 2023-11-01 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id PDBJ Y PDBJ 2009-04-28 REL REL SAM S-ADENOSYLMETHIONINE HOH water 2FRN PDB ENTRY 2FRN PDB experimental model SAM 1 2 SAM SAM 250 A HOH 1 3 HOH HOH 251 A HOH 2 3 HOH HOH 252 A HOH 3 3 HOH HOH 253 A HOH 4 3 HOH HOH 254 A HOH 5 3 HOH HOH 255 A HOH 6 3 HOH HOH 256 A HOH 7 3 HOH HOH 257 A HOH 8 3 HOH HOH 258 A HOH 9 3 HOH HOH 259 A HOH 10 3 HOH HOH 260 A HOH 11 3 HOH HOH 261 A HOH 12 3 HOH HOH 262 A HOH 13 3 HOH HOH 263 A HOH 14 3 HOH HOH 264 A HOH 15 3 HOH HOH 265 A HOH 16 3 HOH HOH 266 A HOH 17 3 HOH HOH 267 A HOH 18 3 HOH HOH 268 A HOH 19 3 HOH HOH 269 A HOH 20 3 HOH HOH 270 A HOH 21 3 HOH HOH 271 A HOH 22 3 HOH HOH 272 A HOH 23 3 HOH HOH 273 A HOH 24 3 HOH HOH 274 A HOH 25 3 HOH HOH 275 A HOH 26 3 HOH HOH 276 A HOH 27 3 HOH HOH 277 A HOH 28 3 HOH HOH 278 A HOH 29 3 HOH HOH 279 A HOH 30 3 HOH HOH 280 A HOH 31 3 HOH HOH 281 A HOH 32 3 HOH HOH 282 A HOH 33 3 HOH HOH 283 A HOH 34 3 HOH HOH 284 A HOH 35 3 HOH HOH 285 A HOH 36 3 HOH HOH 286 A HOH 37 3 HOH HOH 287 A HOH 38 3 HOH HOH 288 A HOH 39 3 HOH HOH 289 A HOH 40 3 HOH HOH 290 A HOH 41 3 HOH HOH 291 A HOH 42 3 HOH HOH 292 A HOH 43 3 HOH HOH 293 A HOH 44 3 HOH HOH 294 A HOH 45 3 HOH HOH 295 A HOH 46 3 HOH HOH 296 A HOH 47 3 HOH HOH 297 A HOH 48 3 HOH HOH 298 A HOH 49 3 HOH HOH 299 A HOH 50 3 HOH HOH 300 A HOH 51 3 HOH HOH 301 A HOH 52 3 HOH HOH 302 A HOH 53 3 HOH HOH 303 A HOH 54 3 HOH HOH 304 A HOH 55 3 HOH HOH 305 A HOH 56 3 HOH HOH 306 A HOH 57 3 HOH HOH 307 A HOH 58 3 HOH HOH 308 A HOH 59 3 HOH HOH 309 A HOH 60 3 HOH HOH 310 A HOH 61 3 HOH HOH 311 A HOH 62 3 HOH HOH 312 A HOH 63 3 HOH HOH 313 A HOH 64 3 HOH HOH 314 A HOH 65 3 HOH HOH 315 A HOH 66 3 HOH HOH 316 A HOH 67 3 HOH HOH 317 A HOH 68 3 HOH HOH 318 A HOH 69 3 HOH HOH 319 A HOH 70 3 HOH HOH 320 A HOH 71 3 HOH HOH 321 A HOH 72 3 HOH HOH 322 A HOH 73 3 HOH HOH 323 A HOH 74 3 HOH HOH 324 A HOH 75 3 HOH HOH 325 A HOH 76 3 HOH HOH 326 A HOH 77 3 HOH HOH 327 A HOH 78 3 HOH HOH 328 A HOH 79 3 HOH HOH 329 A n 1 -22 A n 2 -21 A n 3 -20 A n 4 -19 A n 5 -18 A n 6 -17 A n 7 -16 A n 8 -15 A n 9 -14 A n 10 -13 A n 11 -12 A n 12 -11 A n 13 -10 A n 14 -9 A n 15 -8 A n 16 -7 A n 17 -6 A n 18 -5 A n 19 -4 A n 20 -3 A n 21 -2 A n 22 -1 A n 23 0 A n 24 1 A n 25 2 A n 26 3 A LYS 4 n 27 LYS 4 A TYR 5 n 28 TYR 5 A GLN 6 n 29 GLN 6 A LYS 7 n 30 LYS 7 A ILE 8 n 31 ILE 8 A GLY 9 n 32 GLY 9 A ASP 10 n 33 ASP 10 A VAL 11 n 34 VAL 11 A VAL 12 n 35 VAL 12 A ILE 13 n 36 ILE 13 A VAL 14 n 37 VAL 14 A n 38 15 A n 39 16 A n 40 17 A n 41 18 A n 42 19 A n 43 20 A n 44 21 A n 45 22 A n 46 23 A n 47 24 A n 48 25 A n 49 26 A n 50 27 A n 51 28 A n 52 29 A n 53 30 A n 54 31 A CYS 32 n 55 CYS 32 A LYS 33 n 56 LYS 33 A ALA 34 n 57 ALA 34 A ILE 35 n 58 ILE 35 A LEU 36 n 59 LEU 36 A LEU 37 n 60 LEU 37 A TYR 38 n 61 TYR 38 A THR 39 n 62 THR 39 A n 63 40 A n 64 41 A n 65 42 A n 66 43 A n 67 44 A n 68 45 A n 69 46 A n 70 47 A n 71 48 A n 72 49 A HIS 50 n 73 HIS 50 A VAL 51 n 74 VAL 51 A LYS 52 n 75 LYS 52 A ILE 53 n 76 ILE 53 A LEU 54 n 77 LEU 54 A TYR 55 n 78 TYR 55 A GLY 56 n 79 GLY 56 A LYS 57 n 80 LYS 57 A GLU 58 n 81 GLU 58 A THR 59 n 82 THR 59 A GLU 60 n 83 GLU 60 A THR 61 n 84 THR 61 A ILE 62 n 85 ILE 62 A HIS 63 n 86 HIS 63 A LYS 64 n 87 LYS 64 A GLU 65 n 88 GLU 65 A TYR 66 n 89 TYR 66 A GLY 67 n 90 GLY 67 A CYS 68 n 91 CYS 68 A LEU 69 n 92 LEU 69 A PHE 70 n 93 PHE 70 A LYS 71 n 94 LYS 71 A LEU 72 n 95 LEU 72 A ASP 73 n 96 ASP 73 A VAL 74 n 97 VAL 74 A ALA 75 n 98 ALA 75 A LYS 76 n 99 LYS 76 A ILE 77 n 100 ILE 77 A MET 78 n 101 MET 78 A TRP 79 n 102 TRP 79 A SER 80 n 103 SER 80 A GLN 81 n 104 GLN 81 A GLY 82 n 105 GLY 82 A ASN 83 n 106 ASN 83 A ILE 84 n 107 ILE 84 A GLU 85 n 108 GLU 85 A GLU 86 n 109 GLU 86 A ARG 87 n 110 ARG 87 A LYS 88 n 111 LYS 88 A ARG 89 n 112 ARG 89 A MET 90 n 113 MET 90 A ALA 91 n 114 ALA 91 A PHE 92 n 115 PHE 92 A ILE 93 n 116 ILE 93 A SER 94 n 117 SER 94 A ASN 95 n 118 ASN 95 A GLU 96 n 119 GLU 96 A ASN 97 n 120 ASN 97 A GLU 98 n 121 GLU 98 A VAL 99 n 122 VAL 99 A VAL 100 n 123 VAL 100 A VAL 101 n 124 VAL 101 A ASP 102 n 125 ASP 102 A MET 103 n 126 MET 103 A PHE 104 n 127 PHE 104 A ALA 105 n 128 ALA 105 A GLY 106 n 129 GLY 106 A ILE 107 n 130 ILE 107 A GLY 108 n 131 GLY 108 A TYR 109 n 132 TYR 109 A PHE 110 n 133 PHE 110 A THR 111 n 134 THR 111 A ILE 112 n 135 ILE 112 A PRO 113 n 136 PRO 113 A LEU 114 n 137 LEU 114 A ALA 115 n 138 ALA 115 A LYS 116 n 139 LYS 116 A TYR 117 n 140 TYR 117 A SER 118 n 141 SER 118 A LYS 119 n 142 LYS 119 A PRO 120 n 143 PRO 120 A LYS 121 n 144 LYS 121 A LEU 122 n 145 LEU 122 A VAL 123 n 146 VAL 123 A TYR 124 n 147 TYR 124 A ALA 125 n 148 ALA 125 A ILE 126 n 149 ILE 126 A GLU 127 n 150 GLU 127 A LYS 128 n 151 LYS 128 A ASN 129 n 152 ASN 129 A PRO 130 n 153 PRO 130 A THR 131 n 154 THR 131 A ALA 132 n 155 ALA 132 A TYR 133 n 156 TYR 133 A HIS 134 n 157 HIS 134 A TYR 135 n 158 TYR 135 A LEU 136 n 159 LEU 136 A CYS 137 n 160 CYS 137 A GLU 138 n 161 GLU 138 A ASN 139 n 162 ASN 139 A ILE 140 n 163 ILE 140 A LYS 141 n 164 LYS 141 A LEU 142 n 165 LEU 142 A ASN 143 n 166 ASN 143 A LYS 144 n 167 LYS 144 A LEU 145 n 168 LEU 145 A ASN 146 n 169 ASN 146 A ASN 147 n 170 ASN 147 A VAL 148 n 171 VAL 148 A ILE 149 n 172 ILE 149 A PRO 150 n 173 PRO 150 A ILE 151 n 174 ILE 151 A LEU 152 n 175 LEU 152 A ALA 153 n 176 ALA 153 A ASP 154 n 177 ASP 154 A ASN 155 n 178 ASN 155 A ARG 156 n 179 ARG 156 A ASP 157 n 180 ASP 157 A VAL 158 n 181 VAL 158 A GLU 159 n 182 GLU 159 A LEU 160 n 183 LEU 160 A LYS 161 n 184 LYS 161 A ASP 162 n 185 ASP 162 A VAL 163 n 186 VAL 163 A ALA 164 n 187 ALA 164 A ASP 165 n 188 ASP 165 A ARG 166 n 189 ARG 166 A VAL 167 n 190 VAL 167 A ILE 168 n 191 ILE 168 A MET 169 n 192 MET 169 A GLY 170 n 193 GLY 170 A TYR 171 n 194 TYR 171 A VAL 172 n 195 VAL 172 A HIS 173 n 196 HIS 173 A LYS 174 n 197 LYS 174 A THR 175 n 198 THR 175 A HIS 176 n 199 HIS 176 A LYS 177 n 200 LYS 177 A PHE 178 n 201 PHE 178 A LEU 179 n 202 LEU 179 A ASP 180 n 203 ASP 180 A LYS 181 n 204 LYS 181 A THR 182 n 205 THR 182 A PHE 183 n 206 PHE 183 A GLU 184 n 207 GLU 184 A PHE 185 n 208 PHE 185 A LEU 186 n 209 LEU 186 A LYS 187 n 210 LYS 187 A ASP 188 n 211 ASP 188 A ARG 189 n 212 ARG 189 A GLY 190 n 213 GLY 190 A VAL 191 n 214 VAL 191 A ILE 192 n 215 ILE 192 A HIS 193 n 216 HIS 193 A TYR 194 n 217 TYR 194 A HIS 195 n 218 HIS 195 A GLU 196 n 219 GLU 196 A THR 197 n 220 THR 197 A VAL 198 n 221 VAL 198 A ALA 199 n 222 ALA 199 A GLU 200 n 223 GLU 200 A LYS 201 n 224 LYS 201 A ILE 202 n 225 ILE 202 A MET 203 n 226 MET 203 A TYR 204 n 227 TYR 204 A GLU 205 n 228 GLU 205 A ARG 206 n 229 ARG 206 A PRO 207 n 230 PRO 207 A ILE 208 n 231 ILE 208 A GLU 209 n 232 GLU 209 A ARG 210 n 233 ARG 210 A LEU 211 n 234 LEU 211 A LYS 212 n 235 LYS 212 A PHE 213 n 236 PHE 213 A TYR 214 n 237 TYR 214 A ALA 215 n 238 ALA 215 A GLU 216 n 239 GLU 216 A LYS 217 n 240 LYS 217 A ASN 218 n 241 ASN 218 A GLY 219 n 242 GLY 219 A TYR 220 n 243 TYR 220 A LYS 221 n 244 LYS 221 A LEU 222 n 245 LEU 222 A ILE 223 n 246 ILE 223 A ASP 224 n 247 ASP 224 A TYR 225 n 248 TYR 225 A GLU 226 n 249 GLU 226 A VAL 227 n 250 VAL 227 A ARG 228 n 251 ARG 228 A LYS 229 n 252 LYS 229 A ILE 230 n 253 ILE 230 A LYS 231 n 254 LYS 231 A LYS 232 n 255 LYS 232 A TYR 233 n 256 TYR 233 A ALA 234 n 257 ALA 234 A PRO 235 n 258 PRO 235 A GLY 236 n 259 GLY 236 A VAL 237 n 260 VAL 237 A TRP 238 n 261 TRP 238 A HIS 239 n 262 HIS 239 A VAL 240 n 263 VAL 240 A VAL 241 n 264 VAL 241 A VAL 242 n 265 VAL 242 A ASP 243 n 266 ASP 243 A ALA 244 n 267 ALA 244 A LYS 245 n 268 LYS 245 A PHE 246 n 269 PHE 246 A GLU 247 n 270 GLU 247 A ARG 248 n 271 ARG 248 A ILE 249 n 272 ILE 249 A 2.5150 -0.8462 1.6889 1.5732 -1.4149 0.8995 -0.1183 -0.9234 0.1286 0.5643 0.0939 -0.3198 -0.3959 -0.5337 0.0217 0.4806 0.0101 -0.0308 0.5582 -0.0184 0.3410 refined -18.9826 -3.1402 -9.3365 X-RAY DIFFRACTION 1.4643 -0.9342 0.1048 1.7606 -0.1632 0.3715 0.0141 -0.0369 -0.0817 -0.1865 -0.0454 -0.3001 0.0015 -0.0198 0.0307 0.2175 0.0010 0.0375 0.1792 -0.0013 0.2875 refined -4.4278 -10.6318 -29.3500 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain A 4-80 X-RAY DIFFRACTION 2 chain A 81-249 author_and_software_defined_assembly PISA 1 monomeric 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 GLN 6 A N GLN 29 A O ILE 13 A O ILE 36 A N VAL 14 A N VAL 37 A O LEU 37 A O LEU 60 A N TYR 38 A N TYR 61 A O LYS 52 A O LYS 75 A N HIS 63 A N HIS 86 A O PHE 70 A O PHE 93 A O ILE 151 A O ILE 174 A N ALA 125 A N ALA 148 A O TYR 124 A O TYR 147 A N ASP 102 A N ASP 125 A N VAL 99 A N VAL 122 A O ASP 165 A O ASP 188 A N VAL 167 A N VAL 190 A O HIS 193 A O HIS 216 A N GLU 196 A N GLU 219 A O VAL 240 A O VAL 263 A O LYS 245 A O LYS 268 A N ILE 223 A N ILE 246 1 A MET -22 A MET 1 1 Y 1 A GLY -21 A GLY 2 1 Y 1 A SER -20 A SER 3 1 Y 1 A SER -19 A SER 4 1 Y 1 A HIS -18 A HIS 5 1 Y 1 A HIS -17 A HIS 6 1 Y 1 A HIS -16 A HIS 7 1 Y 1 A HIS -15 A HIS 8 1 Y 1 A HIS -14 A HIS 9 1 Y 1 A HIS -13 A HIS 10 1 Y 1 A SER -12 A SER 11 1 Y 1 A SER -11 A SER 12 1 Y 1 A GLY -10 A GLY 13 1 Y 1 A LEU -9 A LEU 14 1 Y 1 A GLU -8 A GLU 15 1 Y 1 A VAL -7 A VAL 16 1 Y 1 A LEU -6 A LEU 17 1 Y 1 A PHE -5 A PHE 18 1 Y 1 A GLN -4 A GLN 19 1 Y 1 A GLY -3 A GLY 20 1 Y 1 A PRO -2 A PRO 21 1 Y 1 A LEU -1 A LEU 22 1 Y 1 A HIS 0 A HIS 23 1 Y 1 A MET 1 A MET 24 1 Y 1 A GLY 2 A GLY 25 1 Y 1 A ILE 3 A ILE 26 1 Y 1 A LYS 15 A LYS 38 1 Y 1 A LYS 16 A LYS 39 1 Y 1 A GLU 17 A GLU 40 1 Y 1 A LEU 18 A LEU 41 1 Y 1 A SER 19 A SER 42 1 Y 1 A GLU 20 A GLU 43 1 Y 1 A ASP 21 A ASP 44 1 Y 1 A GLU 22 A GLU 45 1 Y 1 A ILE 23 A ILE 46 1 Y 1 A ARG 24 A ARG 47 1 Y 1 A GLU 25 A GLU 48 1 Y 1 A ILE 26 A ILE 49 1 Y 1 A VAL 27 A VAL 50 1 Y 1 A LYS 28 A LYS 51 1 Y 1 A ARG 29 A ARG 52 1 Y 1 A THR 30 A THR 53 1 Y 1 A LYS 31 A LYS 54 1 Y 1 A THR 40 A THR 63 1 Y 1 A GLN 41 A GLN 64 1 Y 1 A ILE 42 A ILE 65 1 Y 1 A THR 43 A THR 66 1 Y 1 A GLY 44 A GLY 67 1 Y 1 A GLU 45 A GLU 68 1 Y 1 A PHE 46 A PHE 69 1 Y 1 A ARG 47 A ARG 70 1 Y 1 A THR 48 A THR 71 1 Y 1 A PRO 49 A PRO 72 1 Y 1 A LYS 33 -129.55 -161.83 1 A SER 94 -110.68 -164.74 0.255 0.2103 0.213 2.005 43.446 1030 19791 5.20 48.89 0.27 1 1.52 MOLECULAR REPLACEMENT 0.90 PDB ENTRY 2FRN 62.574 0.357 2.005 43.446 79 1926 27 0 1820 0.005 1889 0.992 2544 18.566 701 0.079 280 0.003 309 0.3072 0.2503 2.1105 106 2061 37.00 0.3171 0.2306 2.2427 125 2499 45.00 0.2839 0.2255 2.4159 150 2689 49.00 0.2487 0.2024 2.6590 160 2795 51.00 0.2487 0.2110 3.0437 163 2858 52.00 0.2443 0.1974 3.8343 159 2936 54.00 0.2433 0.2054 43.4558 167 2923 53.00 2.0 50 3A27 19841 1 refinement PHENIX data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing MOLREP N Crystal structure of M. jannaschii TYW2 in complex with AdoMet 1 N N 2 N N 3 N N A SER 80 A SER 103 HELX_P A GLY 82 A GLY 105 5 1 3 A ASN 83 A ASN 106 HELX_P A PHE 92 A PHE 115 1 2 10 A PHE 110 A PHE 133 HELX_P A SER 118 A SER 141 1 3 9 A ASN 129 A ASN 152 HELX_P A ASN 143 A ASN 166 1 4 15 A ASP 154 A ASP 177 HELX_P A VAL 158 A VAL 181 5 5 5 A LYS 174 A LYS 197 HELX_P A LYS 177 A LYS 200 5 6 4 A PHE 178 A PHE 201 HELX_P A PHE 185 A PHE 208 1 7 8 A LYS 201 A LYS 224 HELX_P A MET 203 A MET 226 5 8 3 A GLU 205 A GLU 228 HELX_P A ASN 218 A ASN 241 1 9 14 TRANSFERASE Wybutosine modification, TRANSFERASE Y1557_METJA UNP 1 1 Q58952 MGIKYQKIGDVVIVKKELSEDEIREIVKRTKCKAILLYTTQITGEFRTPHVKILYGKETETIHKEYGCLFKLDVAKIMWS QGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVEL KDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHETVAEKIMYERPIERLKFYAEKNGYKLIDYEVRKIKKYAPGVWHV VVDAKFERI 1 249 3A27 1 249 Q58952 A 1 24 272 1 expression tag MET -22 3A27 A Q58952 UNP 1 1 expression tag GLY -21 3A27 A Q58952 UNP 2 1 expression tag SER -20 3A27 A Q58952 UNP 3 1 expression tag SER -19 3A27 A Q58952 UNP 4 1 expression tag HIS -18 3A27 A Q58952 UNP 5 1 expression tag HIS -17 3A27 A Q58952 UNP 6 1 expression tag HIS -16 3A27 A Q58952 UNP 7 1 expression tag HIS -15 3A27 A Q58952 UNP 8 1 expression tag HIS -14 3A27 A Q58952 UNP 9 1 expression tag HIS -13 3A27 A Q58952 UNP 10 1 expression tag SER -12 3A27 A Q58952 UNP 11 1 expression tag SER -11 3A27 A Q58952 UNP 12 1 expression tag GLY -10 3A27 A Q58952 UNP 13 1 expression tag LEU -9 3A27 A Q58952 UNP 14 1 expression tag GLU -8 3A27 A Q58952 UNP 15 1 expression tag VAL -7 3A27 A Q58952 UNP 16 1 expression tag LEU -6 3A27 A Q58952 UNP 17 1 expression tag PHE -5 3A27 A Q58952 UNP 18 1 expression tag GLN -4 3A27 A Q58952 UNP 19 1 expression tag GLY -3 3A27 A Q58952 UNP 20 1 expression tag PRO -2 3A27 A Q58952 UNP 21 1 expression tag LEU -1 3A27 A Q58952 UNP 22 1 expression tag HIS 0 3A27 A Q58952 UNP 23 4 2 7 anti-parallel parallel anti-parallel anti-parallel parallel parallel parallel parallel anti-parallel anti-parallel A GLN 6 A GLN 29 A ILE 8 A ILE 31 A VAL 11 A VAL 34 A VAL 14 A VAL 37 A ILE 35 A ILE 58 A TYR 38 A TYR 61 A LYS 52 A LYS 75 A TYR 55 A TYR 78 A GLU 60 A GLU 83 A GLU 65 A GLU 88 A CYS 68 A CYS 91 A ASP 73 A ASP 96 A VAL 148 A VAL 171 A LEU 152 A LEU 175 A LEU 122 A LEU 145 A GLU 127 A GLU 150 A VAL 99 A VAL 122 A ASP 102 A ASP 125 A ALA 164 A ALA 187 A MET 169 A MET 192 A LEU 186 A LEU 209 A ALA 199 A ALA 222 A VAL 237 A VAL 260 A ARG 248 A ARG 271 A TYR 220 A TYR 243 A ALA 234 A ALA 257 BINDING SITE FOR RESIDUE SAM A 250 A SAM 250 Software 19 A MET 78 A MET 101 19 1_555 A SER 80 A SER 103 19 1_555 A ASN 83 A ASN 106 19 1_555 A ARG 87 A ARG 110 19 1_555 A MET 103 A MET 126 19 1_555 A PHE 104 A PHE 127 19 1_555 A GLY 106 A GLY 129 19 1_555 A TYR 109 A TYR 132 19 1_555 A GLU 127 A GLU 150 19 1_555 A LYS 128 A LYS 151 19 1_555 A ASN 129 A ASN 152 19 1_555 A ALA 153 A ALA 176 19 1_555 A ASP 154 A ASP 177 19 1_555 A ASN 155 A ASN 178 19 1_555 A TYR 171 A TYR 194 19 1_555 A PHE 178 A PHE 201 19 1_555 A HOH 256 C HOH 19 1_555 A HOH 279 C HOH 19 1_555 A HOH 304 C HOH 19 1_555 19 P 21 21 21