data for structural and crystallization communications - example

Example: sample information

Example 1: a GADα/glutarate complex

Based in part on Dutyshev, D. I., Darii, E. L., Fomenkova, N. P., Pechik, I. V., Polyakov, K. M., Nikonov, S. V., Andreeva, N. S. & Sukhareva, B. S. (2005). Structure of Escherichia coli glutamate decarboxylase (GADα) in complex with glutarate at 2.05 Å resolution. Acta Cryst. D61, 230-235 [1XEY].

The E. coli enzyme is pyridoxal phosphate dependent and functions as a hexamer. It is an isozyme: the organism has two genes, gadA and gadB. Glutarate is the chosen substrate analogue.

In the example below, the items in gray are identifiers and qualifiers needed to preserve the mmCIF data structure (and auto-generated during the deposition procedure), or other data items stored in the same category in a PDB deposition, but not normally published in the journal.

Wherever possible, one should distinguish within a CIF between items that are unknown, denoted by a query character (?), and those that are not applicable, denoted by a full stop character (.). The example below tries to preserve this distinction, but PDB depositions may not always be able to provide this discrimination.

_entry.id                                 1XEY

_struct.title    'Complex of E. coli glutamate decarboxylase \a and glutarate'

loop_
    _entity.id
    _entity.type
    _entity.src_method
    _entity.pdbx_description
    _entity.pdbx_formula_weight_exptl
    _entity.pdbx_formula_weight_exptl_meth
    _entity.pdbx_mutation
    _entity.pdbx_modification
    _entity.pdbx_number_of_molecules
    _entity.pdbx_ec
        1 polymer     man 'glutamate decarboxylase alpha' 52769.723 ? . . 2
                                                                       4.1.1.15
        2 non-polymer syn 'acetate ion'                   59.045    ? . . 2   .
        3 non-polymer syn 'pyridoxal-5'-phosphate'        247.144   ? . . 2   .
        4 non-polymer syn 'glutaric acid'                 132.116   ? . . 2   .
        5 water       nat water                           18.015    ? . . 390 .

_struct_biol.details
;   GAD-alpha is a hexamer.  In this structure, the hexamer sits
    on a threefold axis and there are two GAD-alpha monomers
    in the asymmetric unit.  Each binds one PLP covalently and
    one GUA as ligand, and is solvated by one ACT.
;
_struct_biol.pdbx_formula_weight           318312
_struct_biol.pdbx_formula_weight_method
                           'calculated from sequence with coenzyme and ligand'

_entity_poly.entity_id                     1
_entity_poly.pdbx_seq_one_letter_code_can
;
MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSI
NKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCG
PVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDM
HIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRP
AGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLR
LRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT
;
_entity_poly.pdbx_seq_one_letter_code
;
MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSI
NKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCG
PVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDM
HIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRP
AGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLR
LRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT
;

loop_
    _entity_poly_seq.entity_id
    _entity_poly_seq.num
    _entity_poly_seq.mon_id
1 1   MET 1 2   ASP 1 3   GLN 1 4   LYS 1 5   LEU 1 6   LEU 1 7   THR
1 8   ASP 1 9   PHE 1 10  ARG 1 11  SER 1 12  GLU 1 13  LEU 1 14  LEU
1 15  ASP 1 16  SER 1 17  ARG 1 18  PHE 1 19  GLY 1 20  ALA 1 21  LYS
1 22  ALA 1 23  ILE 1 24  SER 1 25  THR 1 26  ILE 1 27  ALA 1 28  GLU
1 29  SER 1 30  LYS 1 31  ARG 1 32  PHE 1 33  PRO 1 34  LEU 1 35  HIS
1 36  GLU 1 37  MET 1 38  ARG 1 39  ASP 1 40  ASP 1 41  VAL 1 42  ALA
1 43  PHE 1 44  GLN 1 45  ILE 1 46  ILE 1 47  ASN 1 48  ASP 1 49  GLU
1 50  LEU 1 51  TYR 1 52  LEU 1 53  ASP 1 54  GLY 1 55  ASN 1 56  ALA
1 57  ARG 1 58  GLN 1 59  ASN 1 60  LEU 1 61  ALA 1 62  THR 1 63  PHE
1 64  CYS 1 65  GLN 1 66  THR 1 67  TRP 1 68  ASP 1 69  ASP 1 70  GLU
1 71  ASN 1 72  VAL 1 73  HIS 1 74  LYS 1 75  LEU 1 76  MET 1 77  ASP
1 78  LEU 1 79  SER 1 80  ILE 1 81  ASN 1 82  LYS 1 83  ASN 1 84  TRP
1 85  ILE 1 86  ASP 1 87  LYS 1 88  GLU 1 89  GLU 1 90  TYR 1 91  PRO
1 92  GLN 1 93  SER 1 94  ALA 1 95  ALA 1 96  ILE 1 97  ASP 1 98  LEU
1 99  ARG 1 100 CYS 1 101 VAL 1 102 ASN 1 103 MET 1 104 VAL 1 105 ALA
1 106 ASP 1 107 LEU 1 108 TRP 1 109 HIS 1 110 ALA 1 111 PRO 1 112 ALA
1 113 PRO 1 114 LYS 1 115 ASN 1 116 GLY 1 117 GLN 1 118 ALA 1 119 VAL
1 120 GLY 1 121 THR 1 122 ASN 1 123 THR 1 124 ILE 1 125 GLY 1 126 SER
1 127 SER 1 128 GLU 1 129 ALA 1 130 CYS 1 131 MET 1 132 LEU 1 133 GLY
1 134 GLY 1 135 MET 1 136 ALA 1 137 MET 1 138 LYS 1 139 TRP 1 140 ARG
1 141 TRP 1 142 ARG 1 143 LYS 1 144 ARG 1 145 MET 1 146 GLU 1 147 ALA
1 148 ALA 1 149 GLY 1 150 LYS 1 151 PRO 1 152 THR 1 153 ASP 1 154 LYS
1 155 PRO 1 156 ASN 1 157 LEU 1 158 VAL 1 159 CYS 1 160 GLY 1 161 PRO
1 162 VAL 1 163 GLN 1 164 ILE 1 165 CYS 1 166 TRP 1 167 HIS 1 168 LYS
1 169 PHE 1 170 ALA 1 171 ARG 1 172 TYR 1 173 TRP 1 174 ASP 1 175 VAL
1 176 GLU 1 177 LEU 1 178 ARG 1 179 GLU 1 180 ILE 1 181 PRO 1 182 MET
1 183 ARG 1 184 PRO 1 185 GLY 1 186 GLN 1 187 LEU 1 188 PHE 1 189 MET
1 190 ASP 1 191 PRO 1 192 LYS 1 193 ARG 1 194 MET 1 195 ILE 1 196 GLU
1 197 ALA 1 198 CYS 1 199 ASP 1 200 GLU 1 201 ASN 1 202 THR 1 203 ILE
1 204 GLY 1 205 VAL 1 206 VAL 1 207 PRO 1 208 THR 1 209 PHE 1 210 GLY
1 211 VAL 1 212 THR 1 213 TYR 1 214 THR 1 215 GLY 1 216 ASN 1 217 TYR
1 218 GLU 1 219 PHE 1 220 PRO 1 221 GLN 1 222 PRO 1 223 LEU 1 224 HIS
1 225 ASP 1 226 ALA 1 227 LEU 1 228 ASP 1 229 LYS 1 230 PHE 1 231 GLN
1 232 ALA 1 233 ASP 1 234 THR 1 235 GLY 1 236 ILE 1 237 ASP 1 238 ILE
1 239 ASP 1 240 MET 1 241 HIS 1 242 ILE 1 243 ASP 1 244 ALA 1 245 ALA
1 246 SER 1 247 GLY 1 248 GLY 1 249 PHE 1 250 LEU 1 251 ALA 1 252 PRO
1 253 PHE 1 254 VAL 1 255 ALA 1 256 PRO 1 257 ASP 1 258 ILE 1 259 VAL
1 260 TRP 1 261 ASP 1 262 PHE 1 263 ARG 1 264 LEU 1 265 PRO 1 266 ARG
1 267 VAL 1 268 LYS 1 269 SER 1 270 ILE 1 271 SER 1 272 ALA 1 273 SER
1 274 GLY 1 275 HIS 1 276 LYS 1 277 PHE 1 278 GLY 1 279 LEU 1 280 ALA
1 281 PRO 1 282 LEU 1 283 GLY 1 284 CYS 1 285 GLY 1 286 TRP 1 287 VAL
1 288 ILE 1 289 TRP 1 290 ARG 1 291 ASP 1 292 GLU 1 293 GLU 1 294 ALA
1 295 LEU 1 296 PRO 1 297 GLN 1 298 GLU 1 299 LEU 1 300 VAL 1 301 PHE
1 302 ASN 1 303 VAL 1 304 ASP 1 305 TYR 1 306 LEU 1 307 GLY 1 308 GLY
1 309 GLN 1 310 ILE 1 311 GLY 1 312 THR 1 313 PHE 1 314 ALA 1 315 ILE
1 316 ASN 1 317 PHE 1 318 SER 1 319 ARG 1 320 PRO 1 321 ALA 1 322 GLY
1 323 GLN 1 324 VAL 1 325 ILE 1 326 ALA 1 327 GLN 1 328 TYR 1 329 TYR
1 330 GLU 1 331 PHE 1 332 LEU 1 333 ARG 1 334 LEU 1 335 GLY 1 336 ARG
1 337 GLU 1 338 GLY 1 339 TYR 1 340 THR 1 341 LYS 1 342 VAL 1 343 GLN
1 344 ASN 1 345 ALA 1 346 SER 1 347 TYR 1 348 GLN 1 349 VAL 1 350 ALA
1 351 ALA 1 352 TYR 1 353 LEU 1 354 ALA 1 355 ASP 1 356 GLU 1 357 ILE
1 358 ALA 1 359 LYS 1 360 LEU 1 361 GLY 1 362 PRO 1 363 TYR 1 364 GLU
1 365 PHE 1 366 ILE 1 367 CYS 1 368 THR 1 369 GLY 1 370 ARG 1 371 PRO
1 372 ASP 1 373 GLU 1 374 GLY 1 375 ILE 1 376 PRO 1 377 ALA 1 378 VAL
1 379 CYS 1 380 PHE 1 381 LYS 1 382 LEU 1 383 LYS 1 384 ASP 1 385 GLY
1 386 GLU 1 387 ASP 1 388 PRO 1 389 GLY 1 390 TYR 1 391 THR 1 392 LEU
1 393 TYR 1 394 ASP 1 395 LEU 1 396 SER 1 397 GLU 1 398 ARG 1 399 LEU
1 400 ARG 1 401 LEU 1 402 ARG 1 403 GLY 1 404 TRP 1 405 GLN 1 406 VAL
1 407 PRO 1 408 ALA 1 409 PHE 1 410 THR 1 411 LEU 1 412 GLY 1 413 GLY
1 414 GLU 1 415 ALA 1 416 THR 1 417 ASP 1 418 ILE 1 419 VAL 1 420 VAL
1 421 MET 1 422 ARG 1 423 ILE 1 424 MET 1 425 CYS 1 426 ARG 1 427 ARG
1 428 GLY 1 429 PHE 1 430 GLU 1 431 MET 1 432 ASP 1 433 PHE 1 434 ALA
1 435 GLU 1 436 LEU 1 437 LEU 1 438 LEU 1 439 GLU 1 440 ASP 1 441 TYR
1 442 LYS 1 443 ALA 1 444 SER 1 445 LEU 1 446 LYS 1 447 TYR 1 448 LEU
1 449 SER 1 450 ASP 1 451 HIS 1 452 PRO 1 453 LYS 1 454 LEU 1 455 GLN
1 456 GLY 1 457 ILE 1 458 ALA 1 459 GLN 1 460 GLN 1 461 ASN 1 462 SER
1 463 PHE 1 464 LYS 1 465 HIS 1 466 THR

loop_
    _pdbx_entity_nonpoly.entity_id
    _pdbx_entity_nonpoly.name
    _pdbx_entity_nonpoly.comp_id
        2 'acetate ion'            ACT
        3 'pyridoxal-5'-phosphate' PLP
        4 'glutaric acid'          GUA
        5 water                    HOH

_struct_ref.id         1
_struct_ref.db_name    SWS
_struct_ref.db_code    DCEA_ECOLI

_entity_src_nat.entity_id                        .
_entity_src_nat.pdbx_organism_scientific         .
_entity_src_nat.strain                           .
_entity_src_nat.details                          .

_entity_src_gen.entity_id                        .
_entity_src_gen.pdbx_gene_src_scientific_name    'Escherichia coli'
_entity_src_gen.pdbx_gene_src_strain             'BL21'
_entity_src_gen.pdbx_gene_src_organ              ?
_entity_src_gen.pdbx_gene_src_atcc               ?
_entity_src_gen.pdbx_gene_src_cellular_location  ?
_entity_src_gen.gene_src_details                 .

How this example will appear in the journal