0.024510 0.000000 0.000000 0.000000 0.024510 0.000000 0.000000 0.000000 0.006031 0.00000 0.00000 0.00000 Lim, K. Zhang, H. Tempczyk, A. Bonander, N. Toedt, J. Howard, A. Eisenstein, E. Herzberg, O. Structure 2 Function Project (S2F) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90 90 90 40.8 40.8 165.8 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 I -1 126.904 IODIDE ION non-polymer 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 C14 H20 N6 O5 S 384.411 n S-ADENOSYL-L-HOMOCYSTEINE 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 I N 184 N N N 185 S C N 186 N C N 187 N O N 188 N C N 189 N C N 190 N C N 191 N C 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 H 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 N C N 211 N C N 212 N C N 213 N C N 214 N N N 215 N O 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 H N 231 N N N 232 S C N 233 N C N 234 N O N 235 N C N 236 N C N 237 N S N 238 N C N 239 N O 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 H N 251 N N N 252 S C N 253 N C N 254 N O N 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C Y 261 N C N 262 N O 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 N N 275 S C N 276 N C N 277 N O N 278 N C N 279 N C N 280 N C 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 H N 288 N H N 289 N H N 290 N H N 291 N N N 292 S C N 293 N C N 294 N C N 295 N S N 296 N C N 297 N O N 298 N O 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 N N 338 S C N 339 N C N 340 N O N 341 N C N 342 N O N 343 N O 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 N N 352 S C N 353 N C N 354 N O N 355 R C N 356 N O N 357 N C N 358 N O 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 H N 367 N H N 368 N N N 369 S C N 370 N C N 371 N O N 372 N C Y 373 N C Y 374 N C Y 375 N C Y 376 N N Y 377 N C Y 378 N C Y 379 N C Y 380 N C Y 381 N C N 382 N O 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 H N 394 N H N 395 N N N 396 S C N 397 N C N 398 N O N 399 N C Y 400 N C Y 401 N C Y 402 N C Y 403 N C Y 404 N C Y 405 N C N 406 N O N 407 N O 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 H N 418 N H N 419 N N N 420 S C N 421 N C N 422 N O N 423 N C N 424 N C N 425 N C N 426 N O 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 H N 437 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 sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N doub N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N 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 Y 310 N sing Y 311 N sing Y 312 N doub N 313 N sing Y 314 N sing Y 315 N sing Y 316 N doub N 317 N sing Y 318 N doub N 319 N sing N 320 N sing Y 321 N sing Y 322 N doub N 323 N sing Y 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 doub 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 sing N 341 N sing N 342 N sing N 343 N sing N 344 N doub 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 sing N 357 N sing N 358 N sing N 359 N sing N 360 N doub N 361 N sing N 362 N sing N 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 doub Y 370 N sing Y 371 N sing N 372 N sing Y 373 N sing Y 374 N doub N 375 N sing Y 376 N doub N 377 N sing Y 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 sing N 385 N sing N 386 N sing N 387 N sing N 388 N doub N 389 N sing N 390 N sing N 391 N sing N 392 N sing Y 393 N doub Y 394 N sing Y 395 N sing N 396 N sing Y 397 N doub N 398 N sing Y 399 N doub N 400 N sing Y 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 sing N 409 N sing N 410 N sing N 411 N sing N 412 N doub 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 sing N 422 N sing N 423 N sing US Proteins PSFGEY 0867 0887-3585 51 56 67 10.1002/prot.10323 12596263 Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a Cofactor Bound at a Site Formed by a Knot 2003 10.2210/pdb1mxi/pdb pdb_00001mxi 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 2001-10-01 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.00 1.0 17-ID APS 1.00 SYNCHROTRON APS BEAMLINE 17-ID 18427.414 Hypothetical tRNA/rRNA methyltransferase HI0766 2.1.1.- 1 man polymer 126.904 IODIDE ION 1 syn non-polymer 384.411 S-ADENOSYL-L-HOMOCYSTEINE 1 syn non-polymer 18.015 water 153 nat water yibK no no MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK A HI0766 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 Haemophilus Escherichia Escherichia coli sample HI0766 727 Haemophilus influenzae 469008 Escherichia coli BL21(DE3) BL21(DE3) PLASMID PET17B 1 1.87 34.27 Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH 4.6 20% PMME 2000, 0.1 M sodium acetate, 0.2 M ammonium acetate, 3 % ethylene glycol, pH 4.6, Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH, temperature 298K 298 Structure 2 Function Project S2F chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2003-02-25 1 1 2008-04-28 1 2 2011-07-13 1 3 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1J85 IS YibK methyltransferase from Haemophilius influenzae (HI0766), apo-methyltransferase with a knot-containing fold Y RCSB Y RCSB 2002-10-02 REL REL IOD IODIDE ION SAH S-ADENOSYL-L-HOMOCYSTEINE HOH water 1J85 PDB 1j85 PDB experimental model I1 2001 2 IOD IOD 2001 A SAH 302 3 SAH SAH 302 A WAT 1001 4 HOH HOH 1001 A WAT 1002 4 HOH HOH 1002 A WAT 1003 4 HOH HOH 1003 A WAT 1004 4 HOH HOH 1004 A WAT 1005 4 HOH HOH 1005 A WAT 1006 4 HOH HOH 1006 A WAT 1007 4 HOH HOH 1007 A WAT 1008 4 HOH HOH 1008 A WAT 1009 4 HOH HOH 1009 A WAT 1010 4 HOH HOH 1010 A WAT 1011 4 HOH HOH 1011 A WAT 1012 4 HOH HOH 1012 A WAT 1013 4 HOH HOH 1013 A WAT 1014 4 HOH HOH 1014 A WAT 1015 4 HOH HOH 1015 A WAT 1016 4 HOH HOH 1016 A WAT 1017 4 HOH HOH 1017 A WAT 1018 4 HOH HOH 1018 A WAT 1019 4 HOH HOH 1019 A WAT 1020 4 HOH HOH 1020 A WAT 1021 4 HOH HOH 1021 A WAT 1022 4 HOH HOH 1022 A WAT 1023 4 HOH HOH 1023 A WAT 1024 4 HOH HOH 1024 A WAT 1025 4 HOH HOH 1025 A WAT 1026 4 HOH HOH 1026 A WAT 1027 4 HOH HOH 1027 A WAT 1028 4 HOH HOH 1028 A WAT 1029 4 HOH HOH 1029 A WAT 1030 4 HOH HOH 1030 A WAT 1031 4 HOH HOH 1031 A WAT 1032 4 HOH HOH 1032 A WAT 1033 4 HOH HOH 1033 A WAT 1034 4 HOH HOH 1034 A WAT 1035 4 HOH HOH 1035 A WAT 1036 4 HOH HOH 1036 A WAT 1037 4 HOH HOH 1037 A WAT 1038 4 HOH HOH 1038 A WAT 1039 4 HOH HOH 1039 A WAT 1040 4 HOH HOH 1040 A WAT 1041 4 HOH HOH 1041 A WAT 1042 4 HOH HOH 1042 A WAT 1043 4 HOH HOH 1043 A WAT 1044 4 HOH HOH 1044 A WAT 1045 4 HOH HOH 1045 A WAT 1046 4 HOH HOH 1046 A WAT 1047 4 HOH HOH 1047 A WAT 1048 4 HOH HOH 1048 A WAT 1049 4 HOH HOH 1049 A WAT 1050 4 HOH HOH 1050 A WAT 1051 4 HOH HOH 1051 A WAT 1052 4 HOH HOH 1052 A WAT 1053 4 HOH HOH 1053 A WAT 1054 4 HOH HOH 1054 A WAT 1055 4 HOH HOH 1055 A WAT 1056 4 HOH HOH 1056 A WAT 1057 4 HOH HOH 1057 A WAT 1058 4 HOH HOH 1058 A WAT 1059 4 HOH HOH 1059 A WAT 1060 4 HOH HOH 1060 A WAT 1061 4 HOH HOH 1061 A WAT 1062 4 HOH HOH 1062 A WAT 1063 4 HOH HOH 1063 A WAT 1064 4 HOH HOH 1064 A WAT 1065 4 HOH HOH 1065 A WAT 1066 4 HOH HOH 1066 A WAT 1067 4 HOH HOH 1067 A WAT 1068 4 HOH HOH 1068 A WAT 1069 4 HOH HOH 1069 A WAT 1070 4 HOH HOH 1070 A WAT 1071 4 HOH HOH 1071 A WAT 1072 4 HOH HOH 1072 A WAT 1073 4 HOH HOH 1073 A WAT 1074 4 HOH HOH 1074 A WAT 1075 4 HOH HOH 1075 A WAT 1076 4 HOH HOH 1076 A WAT 1077 4 HOH HOH 1077 A WAT 1078 4 HOH HOH 1078 A WAT 1079 4 HOH HOH 1079 A WAT 1080 4 HOH HOH 1080 A WAT 1081 4 HOH HOH 1081 A WAT 1082 4 HOH HOH 1082 A WAT 1083 4 HOH HOH 1083 A WAT 1084 4 HOH HOH 1084 A WAT 1085 4 HOH HOH 1085 A WAT 1086 4 HOH HOH 1086 A WAT 1087 4 HOH HOH 1087 A WAT 1088 4 HOH HOH 1088 A WAT 1089 4 HOH HOH 1089 A WAT 1090 4 HOH HOH 1090 A WAT 1091 4 HOH HOH 1091 A WAT 1092 4 HOH HOH 1092 A WAT 1093 4 HOH HOH 1093 A WAT 1094 4 HOH HOH 1094 A WAT 1095 4 HOH HOH 1095 A WAT 1096 4 HOH HOH 1096 A WAT 1097 4 HOH HOH 1097 A WAT 1098 4 HOH HOH 1098 A WAT 1099 4 HOH HOH 1099 A WAT 1100 4 HOH HOH 1100 A WAT 1101 4 HOH HOH 1101 A WAT 1102 4 HOH HOH 1102 A WAT 1103 4 HOH HOH 1103 A WAT 1104 4 HOH HOH 1104 A WAT 1105 4 HOH HOH 1105 A WAT 1106 4 HOH HOH 1106 A WAT 1107 4 HOH HOH 1107 A WAT 1108 4 HOH HOH 1108 A WAT 1109 4 HOH HOH 1109 A WAT 1110 4 HOH HOH 1110 A WAT 1111 4 HOH HOH 1111 A WAT 1112 4 HOH HOH 1112 A WAT 1113 4 HOH HOH 1113 A WAT 1114 4 HOH HOH 1114 A WAT 1115 4 HOH HOH 1115 A WAT 1116 4 HOH HOH 1116 A WAT 1117 4 HOH HOH 1117 A WAT 1118 4 HOH HOH 1118 A WAT 1119 4 HOH HOH 1119 A WAT 1120 4 HOH HOH 1120 A WAT 1121 4 HOH HOH 1121 A WAT 1122 4 HOH HOH 1122 A WAT 1123 4 HOH HOH 1123 A WAT 1124 4 HOH HOH 1124 A WAT 1125 4 HOH HOH 1125 A WAT 1126 4 HOH HOH 1126 A WAT 1127 4 HOH HOH 1127 A WAT 1128 4 HOH HOH 1128 A WAT 1129 4 HOH HOH 1129 A WAT 1130 4 HOH HOH 1130 A WAT 1131 4 HOH HOH 1131 A WAT 1132 4 HOH HOH 1132 A WAT 1133 4 HOH HOH 1133 A WAT 1134 4 HOH HOH 1134 A WAT 1135 4 HOH HOH 1135 A WAT 1136 4 HOH HOH 1136 A WAT 1137 4 HOH HOH 1137 A WAT 1138 4 HOH HOH 1138 A WAT 1139 4 HOH HOH 1139 A WAT 1140 4 HOH HOH 1140 A WAT 1141 4 HOH HOH 1141 A WAT 1142 4 HOH HOH 1142 A WAT 1143 4 HOH HOH 1143 A WAT 1144 4 HOH HOH 1144 A WAT 1145 4 HOH HOH 1145 A WAT 1146 4 HOH HOH 1146 A WAT 1147 4 HOH HOH 1147 A WAT 1148 4 HOH HOH 1148 A WAT 1149 4 HOH HOH 1149 A WAT 1150 4 HOH HOH 1150 A WAT 1151 4 HOH HOH 1151 A WAT 1152 4 HOH HOH 1152 A WAT 1153 4 HOH HOH 1153 A MET 1 n 1 MET 1 A LEU 2 n 2 LEU 2 A ASP 3 n 3 ASP 3 A ILE 4 n 4 ILE 4 A VAL 5 n 5 VAL 5 A LEU 6 n 6 LEU 6 A TYR 7 n 7 TYR 7 A GLU 8 n 8 GLU 8 A PRO 9 n 9 PRO 9 A GLU 10 n 10 GLU 10 A ILE 11 n 11 ILE 11 A PRO 12 n 12 PRO 12 A GLN 13 n 13 GLN 13 A ASN 14 n 14 ASN 14 A THR 15 n 15 THR 15 A GLY 16 n 16 GLY 16 A ASN 17 n 17 ASN 17 A ILE 18 n 18 ILE 18 A ILE 19 n 19 ILE 19 A ARG 20 n 20 ARG 20 A LEU 21 n 21 LEU 21 A CYS 22 n 22 CYS 22 A ALA 23 n 23 ALA 23 A ASN 24 n 24 ASN 24 A THR 25 n 25 THR 25 A GLY 26 n 26 GLY 26 A PHE 27 n 27 PHE 27 A ARG 28 n 28 ARG 28 A LEU 29 n 29 LEU 29 A HIS 30 n 30 HIS 30 A LEU 31 n 31 LEU 31 A ILE 32 n 32 ILE 32 A GLU 33 n 33 GLU 33 A PRO 34 n 34 PRO 34 A LEU 35 n 35 LEU 35 A GLY 36 n 36 GLY 36 A PHE 37 n 37 PHE 37 A THR 38 n 38 THR 38 A TRP 39 n 39 TRP 39 A ASP 40 n 40 ASP 40 A ASP 41 n 41 ASP 41 A LYS 42 n 42 LYS 42 A ARG 43 n 43 ARG 43 A LEU 44 n 44 LEU 44 A ARG 45 n 45 ARG 45 A ARG 46 n 46 ARG 46 A SER 47 n 47 SER 47 A GLY 48 n 48 GLY 48 A LEU 49 n 49 LEU 49 A ASP 50 n 50 ASP 50 A TYR 51 n 51 TYR 51 A HIS 52 n 52 HIS 52 A GLU 53 n 53 GLU 53 A PHE 54 n 54 PHE 54 A ALA 55 n 55 ALA 55 A GLU 56 n 56 GLU 56 A ILE 57 n 57 ILE 57 A LYS 58 n 58 LYS 58 A ARG 59 n 59 ARG 59 A HIS 60 n 60 HIS 60 A LYS 61 n 61 LYS 61 A THR 62 n 62 THR 62 A PHE 63 n 63 PHE 63 A GLU 64 n 64 GLU 64 A ALA 65 n 65 ALA 65 A PHE 66 n 66 PHE 66 A LEU 67 n 67 LEU 67 A GLU 68 n 68 GLU 68 A SER 69 n 69 SER 69 A GLU 70 n 70 GLU 70 A LYS 71 n 71 LYS 71 A PRO 72 n 72 PRO 72 A LYS 73 n 73 LYS 73 A ARG 74 n 74 ARG 74 A LEU 75 n 75 LEU 75 A PHE 76 n 76 PHE 76 A ALA 77 n 77 ALA 77 A LEU 78 n 78 LEU 78 A THR 79 n 79 THR 79 A THR 80 n 80 THR 80 A LYS 81 n 81 LYS 81 A GLY 82 n 82 GLY 82 A CYS 83 n 83 CYS 83 A PRO 84 n 84 PRO 84 A ALA 85 n 85 ALA 85 A HIS 86 n 86 HIS 86 A SER 87 n 87 SER 87 A GLN 88 n 88 GLN 88 A VAL 89 n 89 VAL 89 A LYS 90 n 90 LYS 90 A PHE 91 n 91 PHE 91 A LYS 92 n 92 LYS 92 A LEU 93 n 93 LEU 93 A GLY 94 n 94 GLY 94 A ASP 95 n 95 ASP 95 A TYR 96 n 96 TYR 96 A LEU 97 n 97 LEU 97 A MET 98 n 98 MET 98 A PHE 99 n 99 PHE 99 A GLY 100 n 100 GLY 100 A PRO 101 n 101 PRO 101 A GLU 102 n 102 GLU 102 A THR 103 n 103 THR 103 A ARG 104 n 104 ARG 104 A GLY 105 n 105 GLY 105 A ILE 106 n 106 ILE 106 A PRO 107 n 107 PRO 107 A MET 108 n 108 MET 108 A SER 109 n 109 SER 109 A ILE 110 n 110 ILE 110 A LEU 111 n 111 LEU 111 A ASN 112 n 112 ASN 112 A GLU 113 n 113 GLU 113 A MET 114 n 114 MET 114 A PRO 115 n 115 PRO 115 A MET 116 n 116 MET 116 A GLU 117 n 117 GLU 117 A GLN 118 n 118 GLN 118 A LYS 119 n 119 LYS 119 A ILE 120 n 120 ILE 120 A ARG 121 n 121 ARG 121 A ILE 122 n 122 ILE 122 A PRO 123 n 123 PRO 123 A MET 124 n 124 MET 124 A THR 125 n 125 THR 125 A ALA 126 n 126 ALA 126 A ASN 127 n 127 ASN 127 A SER 128 n 128 SER 128 A ARG 129 n 129 ARG 129 A SER 130 n 130 SER 130 A MET 131 n 131 MET 131 A ASN 132 n 132 ASN 132 A LEU 133 n 133 LEU 133 A SER 134 n 134 SER 134 A ASN 135 n 135 ASN 135 A SER 136 n 136 SER 136 A VAL 137 n 137 VAL 137 A ALA 138 n 138 ALA 138 A VAL 139 n 139 VAL 139 A THR 140 n 140 THR 140 A VAL 141 n 141 VAL 141 A TYR 142 n 142 TYR 142 A GLU 143 n 143 GLU 143 A ALA 144 n 144 ALA 144 A TRP 145 n 145 TRP 145 A ARG 146 n 146 ARG 146 A GLN 147 n 147 GLN 147 A LEU 148 n 148 LEU 148 A GLY 149 n 149 GLY 149 A TYR 150 n 150 TYR 150 A LYS 151 n 151 LYS 151 A GLY 152 n 152 GLY 152 A ALA 153 n 153 ALA 153 A VAL 154 n 154 VAL 154 A ASN 155 n 155 ASN 155 A LEU 156 n 156 LEU 156 A n 157 157 A n 158 158 A n 159 159 A n 160 160 A author_defined_assembly 2 dimeric 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 A O HIS 60 A O HIS 60 A N LEU 31 A N LEU 31 A O ARG 28 A O ARG 28 A N ILE 4 A N ILE 4 A N VAL 5 A N VAL 5 A O LEU 97 A O LEU 97 A O TYR 96 A O TYR 96 A N PHE 76 A N PHE 76 A N ALA 77 A N ALA 77 A O ILE 120 A O ILE 120 1 A PRO 157 A PRO 157 1 Y 1 A GLU 158 A GLU 158 1 Y 1 A VAL 159 A VAL 159 1 Y 1 A LYS 160 A LYS 160 1 Y 1 A ARG 43 -59.09 12.82 1 A PHE 54 -104.51 -162.81 1 A ALA 55 63.34 -16.30 1 A ARG 104 -152.98 -12.25 1 A SER 130 B 176.58 173.08 29 0.254 0.196 1.7 20.0 1593 14742 random 1 isotropic THROUGHOUT 2 MOLECULAR REPLACEMENT PDB 1j85 Engh & Huber 1.7 20.0 153 1479 27 0 1299 0.017 1.8 0.273 0.215 1.78 1.7 50 1MXI 15394 15394 0 0 0.04 1 18.5 93.7 0.223 1.7 1.78 69.2 data reduction DENZO data scaling SCALEPACK refinement CNS phasing CNS Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot 1 N N 2 N N 3 N N 4 N N A ILE 11 A ILE 11 HELX_P A GLY 26 A GLY 26 1 1 16 A ASP 41 A ASP 41 HELX_P A ARG 46 A ARG 46 1 2 6 A ASP 50 A ASP 50 HELX_P A PHE 54 A PHE 54 5 3 5 A THR 62 A THR 62 HELX_P A LYS 71 A LYS 71 1 4 10 A ALA 85 A ALA 85 HELX_P A VAL 89 A VAL 89 5 5 5 A PRO 107 A PRO 107 HELX_P A ASN 112 A ASN 112 1 6 6 A GLU 113 A GLU 113 HELX_P A MET 114 A MET 114 5 7 2 A PRO 115 A PRO 115 HELX_P A GLU 117 A GLU 117 5 8 3 A ASN 132 A ASN 132 HELX_P A LEU 148 A LEU 148 1 9 17 TRANSFERASE methyltransferase, S-adenosylhomocysteine, spoU family, Structure 2 Function Project, S2F, Structural Genomics, TRANSFERASE A GLU 33 A GLU 33 1 A PRO 34 A PRO 34 0.35 Y766_HAEIN UNP 1 1 P44868 MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTT KGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK 1 160 1MXI 1 160 P44868 A 1 1 160 6 parallel parallel parallel parallel parallel A LYS 58 A LYS 58 A HIS 60 A HIS 60 A ARG 28 A ARG 28 A ILE 32 A ILE 32 A ASP 3 A ASP 3 A TYR 7 A TYR 7 A ASP 95 A ASP 95 A PHE 99 A PHE 99 A ARG 74 A ARG 74 A LEU 78 A LEU 78 A LYS 119 A LYS 119 A ILE 120 A ILE 120 BINDING SITE FOR RESIDUE IOD A 2001 A IOD 2001 Software 1 BINDING SITE FOR RESIDUE SAH A 302 A SAH 302 Software 16 A MET 131 A MET 131 1 1_555 A LEU 78 A LEU 78 16 1_555 A THR 79 A THR 79 16 1_555 A THR 80 A THR 80 16 1_555 A PHE 99 A PHE 99 16 1_555 A GLY 100 A GLY 100 16 1_555 A PRO 101 A PRO 101 16 1_555 A GLU 102 A GLU 102 16 1_555 A ARG 104 A ARG 104 16 1_555 A GLY 105 A GLY 105 16 1_555 A ARG 121 A ARG 121 16 1_555 A ILE 122 A ILE 122 16 1_555 A MET 124 A MET 124 16 1_555 A SER 130 A SER 130 16 1_555 A MET 131 A MET 131 16 1_555 A SER 136 A SER 136 16 1_555 A HOH 1002 D HOH 16 1_555 92 P 41 21 2