.007693 .000000 .000354 .000000 .021384 .000000 .000000 .000000 .026078 .00000 .00000 .00000 Richard, S.B. Bowman, M.E. Kwiatkowski, W. Kang, I. Chow, C. Lillo, A. Cane, D.E. Noel, J.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 92.64 90.00 129.990 46.764 38.387 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 C14 H25 N3 O14 P2 521.308 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL non-polymer 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 Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 N C N 76 N N N 77 N C N 78 N C N 79 N C N 80 N O N 81 N N N 82 R C N 83 R C N 84 N O N 85 S C N 86 R C N 87 N O N 88 N O N 89 N C N 90 N O N 91 R P N 92 N O N 93 N O N 94 N O N 95 S P N 96 N O N 97 N O N 98 N O N 99 N C N 100 R C N 101 N O N 102 S C N 103 N C N 104 N C N 105 N O N 106 N O N 107 N H N 108 N H 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 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 H N 132 N N N 133 R C N 134 N C N 135 N O N 136 N C N 137 N S N 138 N O N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N N N 147 S C N 148 N C N 149 N O N 150 N C N 151 N C N 152 N C N 153 N O N 154 N N N 155 N O 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 H N 166 N N N 167 S C N 168 N C N 169 N O N 170 N C N 171 N C N 172 N C N 173 N O N 174 N O N 175 N O 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 H N 184 N H N 185 N N N 186 N C N 187 N C N 188 N O N 189 N O N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N N N 196 S C N 197 N C N 198 N O N 199 N C Y 200 N C Y 201 N N Y 202 N C Y 203 N C Y 204 N N N 205 N O N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N O N 217 N H N 218 N H N 219 N N N 220 S C N 221 N C N 222 N O N 223 S C N 224 N C N 225 N C N 226 N C N 227 N O 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 H N 239 N H N 240 N H N 241 N N N 242 S C N 243 N C N 244 N O N 245 N C N 246 N C N 247 N C N 248 N C N 249 N O 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 H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N N N 264 S C N 265 N C N 266 N O N 267 N C N 268 N C N 269 N C N 270 N C N 271 N N N 272 N O N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H 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 N N 289 S C N 290 N C N 291 N O N 292 N C N 293 N C N 294 N S N 295 N C N 296 N O N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N MG N 309 N N N 310 S C N 311 N C N 312 N O N 313 N C Y 314 N C Y 315 N C Y 316 N C Y 317 N C Y 318 N C Y 319 N C N 320 N O 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 N N 333 S C N 334 N C N 335 N O N 336 N C N 337 N C N 338 N C N 339 N O N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N N N 350 S C N 351 N C N 352 N O N 353 N C N 354 N O N 355 N O N 356 N H 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 N N 364 S C N 365 N C N 366 N O N 367 R C N 368 N O N 369 N C N 370 N O 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 Y 385 N C Y 386 N C Y 387 N C Y 388 N N Y 389 N C Y 390 N C Y 391 N C Y 392 N C Y 393 N C N 394 N O N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N N N 408 S C N 409 N C N 410 N O N 411 N C Y 412 N C Y 413 N C Y 414 N C Y 415 N C Y 416 N C Y 417 N C N 418 N O N 419 N O N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H 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 N N 432 S C N 433 N C N 434 N O N 435 N C N 436 N C N 437 N C N 438 N O N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 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 doub N 75 N doub N 76 N sing N 77 N sing N 78 N doub 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 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 doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing 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 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 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 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 doub 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 doub N 157 N sing N 158 N sing 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 doub 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 doub 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 N 185 N doub 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 doub N 195 N sing N 196 N sing N 197 N sing N 198 N sing Y 199 N sing Y 200 N doub Y 201 N doub N 202 N sing Y 203 N sing N 204 N sing Y 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 doub 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 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 doub N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing 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 doub 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 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 doub N 303 N sing N 304 N sing N 305 N sing N 306 N sing Y 307 N doub Y 308 N sing Y 309 N sing N 310 N sing Y 311 N doub N 312 N sing Y 313 N doub N 314 N sing Y 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 doub 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 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 doub 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 doub N 372 N sing N 373 N sing N 374 N sing N 375 N sing Y 376 N doub Y 377 N sing Y 378 N sing N 379 N sing Y 380 N doub Y 381 N sing Y 382 N sing N 383 N sing Y 384 N sing Y 385 N doub N 386 N sing Y 387 N doub N 388 N sing Y 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 sing N 399 N doub N 400 N sing N 401 N sing N 402 N sing N 403 N sing Y 404 N doub Y 405 N sing Y 406 N sing N 407 N sing Y 408 N doub N 409 N sing Y 410 N doub N 411 N sing Y 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 sing N 422 N sing N 423 N doub 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 US Nat.Struct.Biol. NSBIEW 2024 1072-8368 8 641 648 10.1038/89691 11427897 Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. 2001 10.2210/pdb1ini/pdb pdb_00001ini 1.000000 .000000 .000000 .000000 1.000000 .000000 .000000 .000000 1.000000 .00000 .00000 .00000 100 1 flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) IMAGE PLATE 2001-01-13 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.773 1.0 BL9-1 SSRL 0.773 SYNCHROTRON SSRL BEAMLINE BL9-1 25772.266 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE 2.7.7.- 1 man polymer 24.305 MAGNESIUM ION 1 syn non-polymer 521.308 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL 1 syn non-polymer 18.015 water 103 nat water no no MATTHLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVD GGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGL WHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTRTIHQENT MATTHLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVD GGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGL WHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTRTIHQENT 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 Escherichia Escherichia coli K12 Escherichia Escherichia coli sample ISPD 83333 Escherichia coli 469008 Escherichia coli BL21(DE3) BL21(DE3) PLASMID PHIS8 1 2.26 45.58 VAPOR DIFFUSION, HANGING DROP 6.5 PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K 279 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Derived calculations Source and taxonomy Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2001-11-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2023-08-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CTP AND Mg2+ CRYSTAL STRUCTURE OF THE APO FORM OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS RCSB Y RCSB 2001-05-14 REL REL MG MAGNESIUM ION CDM 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL HOH water 1I52 PDB ENTRY 1I52 PDB experimental model MG2 1 2 MG MG 1002 A PRD 1 3 CDM CDM 1001 A WAT 1 4 HOH HOH 1003 A WAT 2 4 HOH HOH 1004 A WAT 3 4 HOH HOH 1005 A WAT 4 4 HOH HOH 1006 A WAT 5 4 HOH HOH 1007 A WAT 6 4 HOH HOH 1008 A WAT 7 4 HOH HOH 1009 A WAT 8 4 HOH HOH 1010 A WAT 9 4 HOH HOH 1011 A WAT 10 4 HOH HOH 1012 A WAT 11 4 HOH HOH 1013 A WAT 12 4 HOH HOH 1014 A WAT 13 4 HOH HOH 1015 A WAT 14 4 HOH HOH 1016 A WAT 15 4 HOH HOH 1017 A WAT 16 4 HOH HOH 1018 A WAT 17 4 HOH HOH 1019 A WAT 18 4 HOH HOH 1020 A WAT 19 4 HOH HOH 1021 A WAT 20 4 HOH HOH 1022 A WAT 21 4 HOH HOH 1023 A WAT 22 4 HOH HOH 1024 A WAT 23 4 HOH HOH 1025 A WAT 24 4 HOH HOH 1026 A WAT 25 4 HOH HOH 1027 A WAT 26 4 HOH HOH 1028 A WAT 27 4 HOH HOH 1029 A WAT 28 4 HOH HOH 1030 A WAT 29 4 HOH HOH 1031 A WAT 30 4 HOH HOH 1032 A WAT 31 4 HOH HOH 1033 A WAT 32 4 HOH HOH 1034 A WAT 33 4 HOH HOH 1035 A WAT 34 4 HOH HOH 1036 A WAT 35 4 HOH HOH 1037 A WAT 36 4 HOH HOH 1038 A WAT 37 4 HOH HOH 1039 A WAT 38 4 HOH HOH 1040 A WAT 39 4 HOH HOH 1041 A WAT 40 4 HOH HOH 1042 A WAT 41 4 HOH HOH 1043 A WAT 42 4 HOH HOH 1044 A WAT 43 4 HOH HOH 1045 A WAT 44 4 HOH HOH 1046 A WAT 45 4 HOH HOH 1047 A WAT 46 4 HOH HOH 1048 A WAT 47 4 HOH HOH 1049 A WAT 48 4 HOH HOH 1050 A WAT 49 4 HOH HOH 1051 A WAT 50 4 HOH HOH 1052 A WAT 51 4 HOH HOH 1053 A WAT 52 4 HOH HOH 1054 A WAT 53 4 HOH HOH 1055 A WAT 54 4 HOH HOH 1056 A WAT 55 4 HOH HOH 1057 A WAT 56 4 HOH HOH 1058 A WAT 57 4 HOH HOH 1059 A WAT 58 4 HOH HOH 1060 A WAT 59 4 HOH HOH 1061 A WAT 60 4 HOH HOH 1062 A WAT 61 4 HOH HOH 1063 A WAT 62 4 HOH HOH 1064 A WAT 63 4 HOH HOH 1065 A WAT 64 4 HOH HOH 1066 A WAT 65 4 HOH HOH 1067 A WAT 66 4 HOH HOH 1068 A WAT 67 4 HOH HOH 1069 A WAT 68 4 HOH HOH 1070 A WAT 69 4 HOH HOH 1071 A WAT 70 4 HOH HOH 1072 A WAT 71 4 HOH HOH 1073 A WAT 72 4 HOH HOH 1074 A WAT 73 4 HOH HOH 1075 A WAT 74 4 HOH HOH 1076 A WAT 75 4 HOH HOH 1077 A WAT 76 4 HOH HOH 1078 A WAT 77 4 HOH HOH 1079 A WAT 78 4 HOH HOH 1080 A WAT 79 4 HOH HOH 1081 A WAT 80 4 HOH HOH 1082 A WAT 81 4 HOH HOH 1083 A WAT 82 4 HOH HOH 1084 A WAT 83 4 HOH HOH 1085 A WAT 84 4 HOH HOH 1086 A WAT 85 4 HOH HOH 1087 A WAT 86 4 HOH HOH 1088 A WAT 87 4 HOH HOH 1089 A WAT 88 4 HOH HOH 1090 A WAT 89 4 HOH HOH 1091 A WAT 90 4 HOH HOH 1092 A WAT 91 4 HOH HOH 1093 A WAT 92 4 HOH HOH 1094 A WAT 93 4 HOH HOH 1095 A WAT 94 4 HOH HOH 1096 A WAT 95 4 HOH HOH 1097 A WAT 96 4 HOH HOH 1098 A WAT 97 4 HOH HOH 1099 A WAT 98 4 HOH HOH 1100 A WAT 100 4 HOH HOH 1101 A WAT 102 4 HOH HOH 1102 A WAT 103 4 HOH HOH 1103 A WAT 104 4 HOH HOH 1104 A WAT 111 4 HOH HOH 1105 A n 1 1 A n 2 2 A n 3 3 A THR 4 n 4 THR 4 A HIS 5 n 5 HIS 5 A LEU 6 n 6 LEU 6 A ASP 7 n 7 ASP 7 A VAL 8 n 8 VAL 8 A CYS 9 n 9 CYS 9 A ALA 10 n 10 ALA 10 A VAL 11 n 11 VAL 11 A VAL 12 n 12 VAL 12 A PRO 13 n 13 PRO 13 A ALA 14 n 14 ALA 14 A ALA 15 n 15 ALA 15 A GLY 16 n 16 GLY 16 A PHE 17 n 17 PHE 17 A GLY 18 n 18 GLY 18 A ARG 19 n 19 ARG 19 A ARG 20 n 20 ARG 20 A MET 21 n 21 MET 21 A ALA 22 n 22 GLN 22 A THR 23 n 23 THR 23 A GLU 24 n 24 GLU 24 A CYS 25 n 25 CYS 25 A PRO 26 n 26 PRO 26 A LYS 27 n 27 LYS 27 A GLN 28 n 28 GLN 28 A TYR 29 n 29 TYR 29 A LEU 30 n 30 LEU 30 A SER 31 n 31 SER 31 A ILE 32 n 32 ILE 32 A GLY 33 n 33 GLY 33 A ASN 34 n 34 ASN 34 A GLN 35 n 35 GLN 35 A THR 36 n 36 THR 36 A ILE 37 n 37 ILE 37 A LEU 38 n 38 LEU 38 A GLU 39 n 39 GLU 39 A HIS 40 n 40 HIS 40 A SER 41 n 41 SER 41 A VAL 42 n 42 VAL 42 A HIS 43 n 43 HIS 43 A ALA 44 n 44 ALA 44 A LEU 45 n 45 LEU 45 A LEU 46 n 46 LEU 46 A ALA 47 n 47 ALA 47 A HIS 48 n 48 HIS 48 A PRO 49 n 49 PRO 49 A ARG 50 n 50 ARG 50 A VAL 51 n 51 VAL 51 A LYS 52 n 52 LYS 52 A ARG 53 n 53 ARG 53 A VAL 54 n 54 VAL 54 A VAL 55 n 55 VAL 55 A ILE 56 n 56 ILE 56 A ALA 57 n 57 ALA 57 A ILE 58 n 58 ILE 58 A SER 59 n 59 SER 59 A PRO 60 n 60 PRO 60 A GLY 61 n 61 GLY 61 A ASP 62 n 62 ASP 62 A SER 63 n 63 SER 63 A ARG 64 n 64 ARG 64 A PHE 65 n 65 PHE 65 A ALA 66 n 66 ALA 66 A GLN 67 n 67 GLN 67 A LEU 68 n 68 LEU 68 A PRO 69 n 69 PRO 69 A LEU 70 n 70 LEU 70 A ALA 71 n 71 ALA 71 A ASN 72 n 72 ASN 72 A HIS 73 n 73 HIS 73 A PRO 74 n 74 PRO 74 A GLN 75 n 75 GLN 75 A ILE 76 n 76 ILE 76 A THR 77 n 77 THR 77 A VAL 78 n 78 VAL 78 A VAL 79 n 79 VAL 79 A ASP 80 n 80 ASP 80 A GLY 81 n 81 GLY 81 A GLY 82 n 82 GLY 82 A ASP 83 n 83 ASP 83 A GLU 84 n 84 GLU 84 A ARG 85 n 85 ARG 85 A ALA 86 n 86 ALA 86 A ASP 87 n 87 ASP 87 A SER 88 n 88 SER 88 A VAL 89 n 89 VAL 89 A LEU 90 n 90 LEU 90 A ALA 91 n 91 ALA 91 A GLY 92 n 92 GLY 92 A LEU 93 n 93 LEU 93 A LYS 94 n 94 LYS 94 A ALA 95 n 95 ALA 95 A ALA 96 n 96 ALA 96 A GLY 97 n 97 GLY 97 A ASP 98 n 98 ASP 98 A ALA 99 n 99 ALA 99 A GLN 100 n 100 GLN 100 A TRP 101 n 101 TRP 101 A VAL 102 n 102 VAL 102 A LEU 103 n 103 LEU 103 A VAL 104 n 104 VAL 104 A HIS 105 n 105 HIS 105 A ASP 106 n 106 ASP 106 A ALA 107 n 107 ALA 107 A ALA 108 n 108 ALA 108 A ARG 109 n 109 ARG 109 A PRO 110 n 110 PRO 110 A CYS 111 n 111 CYS 111 A LEU 112 n 112 LEU 112 A HIS 113 n 113 HIS 113 A GLN 114 n 114 GLN 114 A ASP 115 n 115 ASP 115 A ASP 116 n 116 ASP 116 A LEU 117 n 117 LEU 117 A ALA 118 n 118 ALA 118 A ARG 119 n 119 ARG 119 A LEU 120 n 120 LEU 120 A LEU 121 n 121 LEU 121 A ALA 122 n 122 ALA 122 A LEU 123 n 123 LEU 123 A SER 124 n 124 SER 124 A GLU 125 n 125 GLU 125 A THR 126 n 126 THR 126 A SER 127 n 127 SER 127 A ARG 128 n 128 ARG 128 A THR 129 n 129 THR 129 A GLY 130 n 130 GLY 130 A GLY 131 n 131 GLY 131 A ILE 132 n 132 ILE 132 A LEU 133 n 133 LEU 133 A ALA 134 n 134 ALA 134 A ALA 135 n 135 ALA 135 A PRO 136 n 136 PRO 136 A VAL 137 n 137 VAL 137 A ARG 138 n 138 ARG 138 A ASP 139 n 139 ASP 139 A THR 140 n 140 THR 140 A MET 141 n 141 MET 141 A LYS 142 n 142 LYS 142 A ARG 143 n 143 ARG 143 A ALA 144 n 144 ALA 144 A GLU 145 n 145 GLU 145 A PRO 146 n 146 PRO 146 A GLY 147 n 147 GLY 147 A LYS 148 n 148 LYS 148 A ASN 149 n 149 ASN 149 A ALA 150 n 150 ALA 150 A ILE 151 n 151 ILE 151 A ALA 152 n 152 ALA 152 A HIS 153 n 153 HIS 153 A THR 154 n 154 THR 154 A VAL 155 n 155 VAL 155 A ASP 156 n 156 ASP 156 A ARG 157 n 157 ARG 157 A ASN 158 n 158 ASN 158 A GLY 159 n 159 GLY 159 A LEU 160 n 160 LEU 160 A TRP 161 n 161 TRP 161 A HIS 162 n 162 HIS 162 A ALA 163 n 163 ALA 163 A LEU 164 n 164 LEU 164 A THR 165 n 165 THR 165 A PRO 166 n 166 PRO 166 A GLN 167 n 167 GLN 167 A PHE 168 n 168 PHE 168 A PHE 169 n 169 PHE 169 A PRO 170 n 170 PRO 170 A ARG 171 n 171 ARG 171 A GLU 172 n 172 GLU 172 A LEU 173 n 173 LEU 173 A LEU 174 n 174 LEU 174 A HIS 175 n 175 HIS 175 A ASP 176 n 176 ASP 176 A CYS 177 n 177 CYS 177 A LEU 178 n 178 LEU 178 A THR 179 n 179 THR 179 A ARG 180 n 180 ARG 180 A ALA 181 n 181 ALA 181 A LEU 182 n 182 LEU 182 A ASN 183 n 183 ASN 183 A GLU 184 n 184 GLU 184 A GLY 185 n 185 GLY 185 A ALA 186 n 186 ALA 186 A THR 187 n 187 THR 187 A ILE 188 n 188 ILE 188 A THR 189 n 189 THR 189 A ASP 190 n 190 ASP 190 A GLU 191 n 191 GLU 191 A ALA 192 n 192 ALA 192 A SER 193 n 193 SER 193 A ALA 194 n 194 ALA 194 A LEU 195 n 195 LEU 195 A GLU 196 n 196 GLU 196 A TYR 197 n 197 TYR 197 A CYS 198 n 198 CYS 198 A GLY 199 n 199 GLY 199 A PHE 200 n 200 PHE 200 A HIS 201 n 201 HIS 201 A PRO 202 n 202 PRO 202 A GLN 203 n 203 GLN 203 A LEU 204 n 204 LEU 204 A VAL 205 n 205 VAL 205 A GLU 206 n 206 GLU 206 A GLY 207 n 207 GLY 207 A ARG 208 n 208 ARG 208 A ALA 209 n 209 ALA 209 A ASP 210 n 210 ASP 210 A ASN 211 n 211 ASN 211 A ILE 212 n 212 ILE 212 A LYS 213 n 213 LYS 213 A VAL 214 n 214 VAL 214 A THR 215 n 215 THR 215 A ARG 216 n 216 ARG 216 A PRO 217 n 217 PRO 217 A GLU 218 n 218 GLU 218 A ASP 219 n 219 ASP 219 A LEU 220 n 220 LEU 220 A ALA 221 n 221 ALA 221 A LEU 222 n 222 LEU 222 A ALA 223 n 223 ALA 223 A GLU 224 n 224 GLU 224 A PHE 225 n 225 PHE 225 A TYR 226 n 226 TYR 226 A LEU 227 n 227 LEU 227 A THR 228 n 228 THR 228 A n 229 229 A n 230 230 A n 231 231 A n 232 232 A n 233 233 A n 234 234 A n 235 235 A n 236 236 A author_and_software_defined_assembly PISA,PQS 2 dimeric 6320 -26 18520 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_656 -x+1,y,-z+1 crystal symmetry operation 128.2218798075 0.0000000000 38.3462582266 A N THR 77 A N THR 77 A O VAL 54 A O VAL 54 A N LYS 52 A N LYS 52 A O VAL 8 A O VAL 8 A N CYS 9 A N CYS 9 A O TRP 101 A O TRP 101 A N VAL 104 A N VAL 104 A O GLN 167 A O GLN 167 A N PHE 168 A N PHE 168 A O GLY 131 A O GLY 131 A N ILE 132 A N ILE 132 A O GLN 203 A O GLN 203 A N ILE 32 A N ILE 32 A O GLN 35 A O GLN 35 A O ARG 143 A O ARG 143 A N ALA 152 A N ALA 152 1 A CG GLN 22 A CG GLN 22 1 Y 1 A CD GLN 22 A CD GLN 22 1 Y 1 A OE1 GLN 22 A OE1 GLN 22 1 Y 1 A NE2 GLN 22 A NE2 GLN 22 1 Y 1 A MET 1 A MET 1 1 Y 1 A ALA 2 A ALA 2 1 Y 1 A THR 3 A THR 3 1 Y 1 A ARG 229 A ARG 229 1 Y 1 A THR 230 A THR 230 1 Y 1 A ILE 231 A ILE 231 1 Y 1 A HIS 232 A HIS 232 1 Y 1 A GLN 233 A GLN 233 1 Y 1 A GLU 234 A GLU 234 1 Y 1 A ASN 235 A ASN 235 1 Y 1 A THR 236 A THR 236 1 Y 1 A A O O HOH HOH 1068 1068 1.78 1_555 2_656 1 A A O O HOH HOH 1024 1050 1.96 1_555 2_656 1 A ALA 14 -140.35 34.88 1 A ARG 20 -161.80 6.49 1 A GLN 22 69.67 -51.42 1 A ASN 34 -98.21 35.43 1 A ARG 109 -117.39 79.90 1 A THR 126 -143.36 -2.63 1 A PRO 146 -28.50 -70.16 1 A ASN 149 -103.56 44.88 1 A LEU 164 -120.74 -167.69 36.2 -7.95 .00 -1.83 5.00 .00 2.95 0.273 .009 0.222 0.222 1.82 44.00 866 17144 17144 5.1 82.9 RANDOM 2293940.68 .00 1 RESTRAINED THROUGHOUT 00 0 FOURIER SYNTHESIS PDB ENTRY 1I52 FLAT MODEL 44.77 .3689 .30 .23 5.00 .19 .11 1.82 44.00 103 1853 34 0 1716 .009 1.4 24.3 .89 3.30 1.50 4.30 2.00 4.64 2.00 5.84 2.50 0.325 .034 0.239 1.93 92 1894 1894 6 4.6 57.9 21.6 1.80 90.0 1INI 20268 20268 1 1 0.026 0.026 1 26.4 2.8 98.6 1.81 1.83 2.7 641 0.308 1 2.9 98.6 data reduction DENZO data scaling SCALEPACK refinement CNS phasing CNS CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+ 1 N N 2 N N 3 N N 4 N N A PRO 26 A PRO 26 HELX_P A TYR 29 A TYR 29 5 1 4 A ILE 37 A ILE 37 HELX_P A ALA 47 A ALA 47 1 2 11 A ARG 64 A ARG 64 HELX_P A LEU 68 A LEU 68 5 3 5 A LEU 68 A LEU 68 HELX_P A HIS 73 A HIS 73 5 4 6 A GLU 84 A GLU 84 HELX_P A LYS 94 A LYS 94 1 5 11 A HIS 113 A HIS 113 HELX_P A ALA 122 A ALA 122 1 6 10 A LEU 123 A LEU 123 HELX_P A THR 126 A THR 126 5 7 4 A ARG 171 A ARG 171 HELX_P A GLU 184 A GLU 184 1 8 14 A ASP 190 A ASP 190 HELX_P A CYS 198 A CYS 198 1 9 9 A ARG 216 A ARG 216 HELX_P A LEU 227 A LEU 227 1 10 12 metalc 2.666 A CDM 1001 C O2A CDM 1_555 A MG 1002 B MG MG 1_555 TRANSFERASE YGBP, CYTIDYLYLTRANSFERASE, DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP), ISOPRENOID BIOSYNTHESIS, CDPME, MG, TRANSFERASE A THR 165 A THR 165 1 A PRO 166 A PRO 166 0.21 ISPD_ECOLI UNP 1 1 Q46893 MATTHLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVD GGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGL WHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTRTIHQENT 1 236 1INI 1 236 Q46893 A 1 1 236 7 2 2 parallel parallel parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A ILE 76 A ILE 76 A ASP 80 A ASP 80 A VAL 51 A VAL 51 A ILE 58 A ILE 58 A VAL 8 A VAL 8 A PRO 13 A PRO 13 A TRP 101 A TRP 101 A VAL 104 A VAL 104 A TRP 161 A TRP 161 A PRO 170 A PRO 170 A GLY 131 A GLY 131 A PRO 136 A PRO 136 A GLN 203 A GLN 203 A GLU 206 A GLU 206 A SER 31 A SER 31 A ILE 32 A ILE 32 A GLN 35 A GLN 35 A THR 36 A THR 36 A MET 141 A MET 141 A ALA 144 A ALA 144 A ILE 151 A ILE 151 A VAL 155 A VAL 155 BINDING SITE FOR RESIDUE MG A 1002 A MG 1002 Software 2 BINDING SITE FOR RESIDUE CDM A 1001 A CDM 1001 Software 23 A ARG 20 A ARG 20 2 1_555 A CDM 1001 C CDM 2 1_555 A PRO 13 A PRO 13 23 1_555 A ALA 14 A ALA 14 23 1_555 A ALA 15 A ALA 15 23 1_555 A GLY 16 A GLY 16 23 1_555 A ARG 20 A ARG 20 23 1_555 A LYS 27 A LYS 27 23 1_555 A GLY 82 A GLY 82 23 1_555 A ASP 83 A ASP 83 23 1_555 A GLU 84 A GLU 84 23 1_555 A ARG 85 A ARG 85 23 1_555 A SER 88 A SER 88 23 1_555 A ASP 106 A ASP 106 23 1_555 A ALA 107 A ALA 107 23 1_555 A ALA 108 A ALA 108 23 1_555 A ARG 109 A ARG 109 23 1_555 A ASP 139 A ASP 139 23 2_656 A THR 140 A THR 140 23 2_656 A ARG 157 A ARG 157 23 2_656 A ALA 163 A ALA 163 23 1_555 A THR 189 A THR 189 23 1_555 A LYS 213 A LYS 213 23 1_555 A THR 215 A THR 215 23 1_555 A MG 1002 B MG 23 1_555 5 C 1 2 1