[English] 日本語
Yorodumi
- PDB-3git: Crystal structure of a truncated acetyl-CoA synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3git
TitleCrystal structure of a truncated acetyl-CoA synthase
ComponentsCarbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
KeywordsTRANSFERASE / acetyltransferase / Carbon dioxide fixation / Iron / Iron-sulfur / Metal-binding / Nickel
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / carbon-monoxide dehydrogenase (acceptor) activity / acetyl-CoA metabolic process / carbon fixation / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal ...Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsVolbeda, A. / Darnault, C. / Fontecilla-Camps, J.C.
CitationJournal: Biochemistry / Year: 2009
Title: Novel domain arrangement in the crystal structure of a truncated acetyl-CoA synthase from Moorella thermoacetica
Authors: Volbeda, A. / Darnault, C. / Tan, X. / Lindahl, P.A. / Fontecilla-Camps, J.C.
History
DepositionMar 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
E: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
F: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,25554
Polymers286,6906
Non-polymers5,56548
Water3,405189
1
A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,80510
Polymers47,7821
Non-polymers1,0249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7099
Polymers47,7821
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7099
Polymers47,7821
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7099
Polymers47,7821
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6138
Polymers47,7821
Non-polymers8317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7099
Polymers47,7821
Non-polymers9278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-705 kcal/mol
Surface area91540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.400, 166.400, 245.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUGLUGLU1AA318 - 3588 - 48
211LEULEUGLUGLU1BB318 - 3588 - 48
311LEULEUGLUGLU1CC318 - 3588 - 48
411LEULEUGLUGLU1DD318 - 3588 - 48
511LEULEUGLUGLU1EE318 - 3588 - 48
611LEULEUGLUGLU1FF318 - 3588 - 48
121GLUGLUILEILE1AA360 - 36650 - 56
221GLUGLUILEILE1BB360 - 36650 - 56
321GLUGLUILEILE1CC360 - 36650 - 56
421GLUGLUILEILE1DD360 - 36650 - 56
521GLUGLUILEILE1EE360 - 36650 - 56
621GLUGLUILEILE1FF360 - 36650 - 56
131VALVALSERSER1AA368 - 38058 - 70
231VALVALSERSER1BB368 - 38058 - 70
331VALVALSERSER1CC368 - 38058 - 70
431VALVALSERSER1DD368 - 38058 - 70
531VALVALSERSER1EE368 - 38058 - 70
631VALVALSERSER1FF368 - 38058 - 70
141LEULEUGLYGLY1AA382 - 39272 - 82
241LEULEUGLYGLY1BB382 - 39272 - 82
341LEULEUGLYGLY1CC382 - 39272 - 82
441LEULEUGLYGLY1DD382 - 39272 - 82
541LEULEUGLYGLY1EE382 - 39272 - 82
641LEULEUGLYGLY1FF382 - 39272 - 82
151PHEPHELYSLYS1AA399 - 45389 - 143
251PHEPHELYSLYS1BB399 - 45389 - 143
351PHEPHELYSLYS1CC399 - 45389 - 143
451PHEPHELYSLYS1DD399 - 45389 - 143
551PHEPHELYSLYS1EE399 - 45389 - 143
651PHEPHELYSLYS1FF399 - 45389 - 143
161GLUGLUALAALA1AA455 - 458145 - 148
261GLUGLUALAALA1BB455 - 458145 - 148
361GLUGLUALAALA1CC455 - 458145 - 148
461GLUGLUALAALA1DD455 - 458145 - 148
561GLUGLUALAALA1EE455 - 458145 - 148
661GLUGLUALAALA1FF455 - 458145 - 148
171VALVALTHRTHR1AA463 - 469153 - 159
271VALVALTHRTHR1BB463 - 469153 - 159
371VALVALTHRTHR1CC463 - 469153 - 159
471VALVALTHRTHR1DD463 - 469153 - 159
571VALVALTHRTHR1EE463 - 469153 - 159
671VALVALTHRTHR1FF463 - 469153 - 159
181GLUGLUVALVAL1AA471 - 474161 - 164
281GLUGLUVALVAL1BB471 - 474161 - 164
381GLUGLUVALVAL1CC471 - 474161 - 164
481GLUGLUVALVAL1DD471 - 474161 - 164
581GLUGLUVALVAL1EE471 - 474161 - 164
681GLUGLUVALVAL1FF471 - 474161 - 164
191GLUGLUARGARG1AA476 - 482166 - 172
291GLUGLUARGARG1BB476 - 482166 - 172
391GLUGLUARGARG1CC476 - 482166 - 172
491GLUGLUARGARG1DD476 - 482166 - 172
591GLUGLUARGARG1EE476 - 482166 - 172
691GLUGLUARGARG1FF476 - 482166 - 172
1101TYRTYRASPASP1AA485 - 490175 - 180
2101TYRTYRASPASP1BB485 - 490175 - 180
3101TYRTYRASPASP1CC485 - 490175 - 180
4101TYRTYRASPASP1DD485 - 490175 - 180
5101TYRTYRASPASP1EE485 - 490175 - 180
6101TYRTYRASPASP1FF485 - 490175 - 180
1111GLYGLYASPASP1AA494 - 497184 - 187
2111GLYGLYASPASP1BB494 - 497184 - 187
3111GLYGLYASPASP1CC494 - 497184 - 187
4111GLYGLYASPASP1DD494 - 497184 - 187
5111GLYGLYASPASP1EE494 - 497184 - 187
6111GLYGLYASPASP1FF494 - 497184 - 187
1121PHEPHEALAALA1AA503 - 536193 - 226
2121PHEPHEALAALA1BB503 - 536193 - 226
3121PHEPHEALAALA1CC503 - 536193 - 226
4121PHEPHEALAALA1DD503 - 536193 - 226
5121PHEPHEALAALA1EE503 - 536193 - 226
6121PHEPHEALAALA1FF503 - 536193 - 226
1131ALAALALYSLYS1AA538 - 553228 - 243
2131ALAALALYSLYS1BB538 - 553228 - 243
3131ALAALALYSLYS1CC538 - 553228 - 243
4131ALAALALYSLYS1DD538 - 553228 - 243
5131ALAALALYSLYS1EE538 - 553228 - 243
6131ALAALALYSLYS1FF538 - 553228 - 243
1141GLYGLYTRPTRP1AA555 - 564245 - 254
2141GLYGLYTRPTRP1BB555 - 564245 - 254
3141GLYGLYTRPTRP1CC555 - 564245 - 254
4141GLYGLYTRPTRP1DD555 - 564245 - 254
5141GLYGLYTRPTRP1EE555 - 564245 - 254
6141GLYGLYTRPTRP1FF555 - 564245 - 254
1151VALVALASPASP1AA567 - 569257 - 259
2151VALVALASPASP1BB567 - 569257 - 259
3151VALVALASPASP1CC567 - 569257 - 259
4151VALVALASPASP1DD567 - 569257 - 259
5151VALVALASPASP1EE567 - 569257 - 259
6151VALVALASPASP1FF567 - 569257 - 259
1161LEULEUASNASN1AA571 - 576261 - 266
2161LEULEUASNASN1BB571 - 576261 - 266
3161LEULEUASNASN1CC571 - 576261 - 266
4161LEULEUASNASN1DD571 - 576261 - 266
5161LEULEUASNASN1EE571 - 576261 - 266
6161LEULEUASNASN1FF571 - 576261 - 266
1171GLNGLNCYSCYS1AA581 - 583271 - 273
2171GLNGLNCYSCYS1BB581 - 583271 - 273
3171GLNGLNCYSCYS1CC581 - 583271 - 273
4171GLNGLNCYSCYS1DD581 - 583271 - 273
5171GLNGLNCYSCYS1EE581 - 583271 - 273
6171GLNGLNCYSCYS1FF581 - 583271 - 273
1181TYRTYRPROPRO1AA585 - 591275 - 281
2181TYRTYRPROPRO1BB585 - 591275 - 281
3181TYRTYRPROPRO1CC585 - 591275 - 281
4181TYRTYRPROPRO1DD585 - 591275 - 281
5181TYRTYRPROPRO1EE585 - 591275 - 281
6181TYRTYRPROPRO1FF585 - 591275 - 281
1191THRTHRGLYGLY1AA593 - 620283 - 310
2191THRTHRGLYGLY1BB593 - 620283 - 310
3191THRTHRGLYGLY1CC593 - 620283 - 310
4191THRTHRGLYGLY1DD593 - 620283 - 310
5191THRTHRGLYGLY1EE593 - 620283 - 310
6191THRTHRGLYGLY1FF593 - 620283 - 310
1201THRTHRGLYGLY1AA622 - 625312 - 315
2201THRTHRGLYGLY1BB622 - 625312 - 315
3201THRTHRGLYGLY1CC622 - 625312 - 315
4201THRTHRGLYGLY1DD622 - 625312 - 315
5201THRTHRGLYGLY1EE622 - 625312 - 315
6201THRTHRGLYGLY1FF622 - 625312 - 315
1211THRTHRGLYGLY1AA627 - 633317 - 323
2211THRTHRGLYGLY1BB627 - 633317 - 323
3211THRTHRGLYGLY1CC627 - 633317 - 323
4211THRTHRGLYGLY1DD627 - 633317 - 323
5211THRTHRGLYGLY1EE627 - 633317 - 323
6211THRTHRGLYGLY1FF627 - 633317 - 323
1221ILEILEGLYGLY1AA635 - 638325 - 328
2221ILEILEGLYGLY1BB635 - 638325 - 328
3221ILEILEGLYGLY1CC635 - 638325 - 328
4221ILEILEGLYGLY1DD635 - 638325 - 328
5221ILEILEGLYGLY1EE635 - 638325 - 328
6221ILEILEGLYGLY1FF635 - 638325 - 328
1231THRTHRSERSER1AA641 - 654331 - 344
2231THRTHRSERSER1BB641 - 654331 - 344
3231THRTHRSERSER1CC641 - 654331 - 344
4231THRTHRSERSER1DD641 - 654331 - 344
5231THRTHRSERSER1EE641 - 654331 - 344
6231THRTHRSERSER1FF641 - 654331 - 344
1241LYSLYSARGARG1AA656 - 666346 - 356
2241LYSLYSARGARG1BB656 - 666346 - 356
3241LYSLYSARGARG1CC656 - 666346 - 356
4241LYSLYSARGARG1DD656 - 666346 - 356
5241LYSLYSARGARG1EE656 - 666346 - 356
6241LYSLYSARGARG1FF656 - 666346 - 356
1251VALVALTRPTRP1AA668 - 669358 - 359
2251VALVALTRPTRP1BB668 - 669358 - 359
3251VALVALTRPTRP1CC668 - 669358 - 359
4251VALVALTRPTRP1DD668 - 669358 - 359
5251VALVALTRPTRP1EE668 - 669358 - 359
6251VALVALTRPTRP1FF668 - 669358 - 359
1261PROPROVALVAL1AA671 - 683361 - 373
2261PROPROVALVAL1BB671 - 683361 - 373
3261PROPROVALVAL1CC671 - 683361 - 373
4261PROPROVALVAL1DD671 - 683361 - 373
5261PROPROVALVAL1EE671 - 683361 - 373
6261PROPROVALVAL1FF671 - 683361 - 373
1271PHEPHETHRTHR1AA695 - 703385 - 393
2271PHEPHETHRTHR1BB695 - 703385 - 393
3271PHEPHETHRTHR1CC695 - 703385 - 393
4271PHEPHETHRTHR1DD695 - 703385 - 393
5271PHEPHETHRTHR1EE695 - 703385 - 393
6271PHEPHETHRTHR1FF695 - 703385 - 393
1281GLYGLYTHRTHR1AA705 - 707395 - 397
2281GLYGLYTHRTHR1BB705 - 707395 - 397
3281GLYGLYTHRTHR1CC705 - 707395 - 397
4281GLYGLYTHRTHR1DD705 - 707395 - 397
5281GLYGLYTHRTHR1EE705 - 707395 - 397
6281GLYGLYTHRTHR1FF705 - 707395 - 397
1291ASPASPLEULEU1AA709 - 715399 - 405
2291ASPASPLEULEU1BB709 - 715399 - 405
3291ASPASPLEULEU1CC709 - 715399 - 405
4291ASPASPLEULEU1DD709 - 715399 - 405
5291ASPASPLEULEU1EE709 - 715399 - 405
6291ASPASPLEULEU1FF709 - 715399 - 405
1301HISHISMETMET1AA720 - 729410 - 419
2301HISHISMETMET1BB720 - 729410 - 419
3301HISHISMETMET1CC720 - 729410 - 419
4301HISHISMETMET1DD720 - 729410 - 419
5301HISHISMETMET1EE720 - 729410 - 419
6301HISHISMETMET1FF720 - 729410 - 419
1311SF4SF4H2SH2S1AG - I738 - 740
2311SF4SF4H2SH2S1BP - R738 - 740
3311SF4SF4H2SH2S1CX - Z738 - 740
4311SF4SF4H2SH2S1DGA - IA738 - 740
5311SF4SF4H2SH2S1ENA - PA738 - 740
6311SF4SF4H2SH2S1FVA - XA738 - 740
112ILEILELYSLYS3AA316 - 3176 - 7
212ILEILELYSLYS3BB316 - 3176 - 7
312ILEILELYSLYS3CC316 - 3176 - 7
412ILEILELYSLYS3DD316 - 3176 - 7
512ILEILELYSLYS3EE316 - 3176 - 7
612ILEILELYSLYS3FF316 - 3176 - 7
122SERSERSERSER3AA35949
222SERSERSERSER3BB35949
322SERSERSERSER3CC35949
422SERSERSERSER3DD35949
522SERSERSERSER3EE35949
622SERSERSERSER3FF35949
132GLUGLUGLUGLU3AA36757
232GLUGLUGLUGLU3BB36757
332GLUGLUGLUGLU3CC36757
432GLUGLUGLUGLU3DD36757
532GLUGLUGLUGLU3EE36757
632GLUGLUGLUGLU3FF36757
142LYSLYSLYSLYS3AA38171
242LYSLYSLYSLYS3BB38171
342LYSLYSLYSLYS3CC38171
442LYSLYSLYSLYS3DD38171
542LYSLYSLYSLYS3EE38171
642LYSLYSLYSLYS3FF38171
152ARGARGASPASP3AA393 - 39883 - 88
252ARGARGASPASP3BB393 - 39883 - 88
352ARGARGASPASP3CC393 - 39883 - 88
452ARGARGASPASP3DD393 - 39883 - 88
552ARGARGASPASP3EE393 - 39883 - 88
652ARGARGASPASP3FF393 - 39883 - 88
162GLUGLUGLUGLU3AA454144
262GLUGLUGLUGLU3BB454144
362GLUGLUGLUGLU3CC454144
462GLUGLUGLUGLU3DD454144
562GLUGLUGLUGLU3EE454144
662GLUGLUGLUGLU3FF454144
172ILEILEARGARG3AA459 - 462149 - 152
272ILEILEARGARG3BB459 - 462149 - 152
372ILEILEARGARG3CC459 - 462149 - 152
472ILEILEARGARG3DD459 - 462149 - 152
572ILEILEARGARG3EE459 - 462149 - 152
672ILEILEARGARG3FF459 - 462149 - 152
182ASPASPASPASP3AA470160
282ASPASPASPASP3BB470160
382ASPASPASPASP3CC470160
482ASPASPASPASP3DD470160
582ASPASPASPASP3EE470160
682ASPASPASPASP3FF470160
192LYSLYSLYSLYS3AA475165
292LYSLYSLYSLYS3BB475165
392LYSLYSLYSLYS3CC475165
492LYSLYSLYSLYS3DD475165
592LYSLYSLYSLYS3EE475165
692LYSLYSLYSLYS3FF475165
1102GLUGLULYSLYS3AA483 - 484173 - 174
2102GLUGLULYSLYS3BB483 - 484173 - 174
3102GLUGLULYSLYS3CC483 - 484173 - 174
4102GLUGLULYSLYS3DD483 - 484173 - 174
5102GLUGLULYSLYS3EE483 - 484173 - 174
6102GLUGLULYSLYS3FF483 - 484173 - 174
1112ARGARGARGARG3AA491 - 493181 - 183
2112ARGARGARGARG3BB491 - 493181 - 183
3112ARGARGARGARG3CC491 - 493181 - 183
4112ARGARGARGARG3DD491 - 493181 - 183
5112ARGARGARGARG3EE491 - 493181 - 183
6112ARGARGARGARG3FF491 - 493181 - 183
1122GLUGLUTHRTHR3AA498 - 502188 - 192
2122GLUGLUTHRTHR3BB498 - 502188 - 192
3122GLUGLUTHRTHR3CC498 - 502188 - 192
4122GLUGLUTHRTHR3DD498 - 502188 - 192
5122GLUGLUTHRTHR3EE498 - 502188 - 192
6122GLUGLUTHRTHR3FF498 - 502188 - 192
1132LYSLYSLYSLYS3AA537227
2132LYSLYSLYSLYS3BB537227
3132LYSLYSLYSLYS3CC537227
4132LYSLYSLYSLYS3DD537227
5132LYSLYSLYSLYS3EE537227
6132LYSLYSLYSLYS3FF537227
1142GLUGLUGLUGLU3AA554244
2142GLUGLUGLUGLU3BB554244
3142GLUGLUGLUGLU3CC554244
4142GLUGLUGLUGLU3DD554244
5142GLUGLUGLUGLU3EE554244
6142GLUGLUGLUGLU3FF554244
1152LYSLYSSERSER3AA565 - 566255 - 256
2152LYSLYSSERSER3BB565 - 566255 - 256
3152LYSLYSSERSER3CC565 - 566255 - 256
4152LYSLYSSERSER3DD565 - 566255 - 256
5152LYSLYSSERSER3EE565 - 566255 - 256
6152LYSLYSSERSER3FF565 - 566255 - 256
1162TYRTYRTYRTYR3AA570260
2162TYRTYRTYRTYR3BB570260
3162TYRTYRTYRTYR3CC570260
4162TYRTYRTYRTYR3DD570260
5162TYRTYRTYRTYR3EE570260
6162TYRTYRTYRTYR3FF570260
1172ARGARGGLUGLU3AA577 - 580267 - 270
2172ARGARGGLUGLU3BB577 - 580267 - 270
3172ARGARGGLUGLU3CC577 - 580267 - 270
4172ARGARGGLUGLU3DD577 - 580267 - 270
5172ARGARGGLUGLU3EE577 - 580267 - 270
6172ARGARGGLUGLU3FF577 - 580267 - 270
1182LEULEULEULEU3AA584274
2182LEULEULEULEU3BB584274
3182LEULEULEULEU3CC584274
4182LEULEULEULEU3DD584274
5182LEULEULEULEU3EE584274
6182LEULEULEULEU3FF584274
1192METMETMETMET3AA592282
2192METMETMETMET3BB592282
3192METMETMETMET3CC592282
4192METMETMETMET3DD592282
5192METMETMETMET3EE592282
6192METMETMETMET3FF592282
1202METMETMETMET3AA621311
2202METMETMETMET3BB621311
3202METMETMETMET3CC621311
4202METMETMETMET3DD621311
5202METMETMETMET3EE621311
6202METMETMETMET3FF621311
1212METMETMETMET3AA626316
2212METMETMETMET3BB626316
3212METMETMETMET3CC626316
4212METMETMETMET3DD626316
5212METMETMETMET3EE626316
6212METMETMETMET3FF626316
1222METMETMETMET3AA634324
2222METMETMETMET3BB634324
3222METMETMETMET3CC634324
4222METMETMETMET3DD634324
5222METMETMETMET3EE634324
6222METMETMETMET3FF634324
1232THRTHRTHRTHR3AA639329
2232THRTHRTHRTHR3BB639329
3232THRTHRTHRTHR3CC639329
4232THRTHRTHRTHR3DD639329
5232THRTHRTHRTHR3EE639329
6232THRTHRTHRTHR3FF639329
1242LYSLYSLYSLYS3AA655345
2242LYSLYSLYSLYS3BB655345
3242LYSLYSLYSLYS3CC655345
4242LYSLYSLYSLYS3DD655345
5242LYSLYSLYSLYS3EE655345
6242LYSLYSLYSLYS3FF655345
1252ILEILEILEILE3AA667357
2252ILEILEILEILE3BB667357
3252ILEILEILEILE3CC667357
4252ILEILEILEILE3DD667357
5252ILEILEILEILE3EE667357
6252ILEILEILEILE3FF667357
1262METMETMETMET3AA670360
2262METMETMETMET3BB670360
3262METMETMETMET3CC670360
4262METMETMETMET3DD670360
5262METMETMETMET3EE670360
6262METMETMETMET3FF670360
1272ARGARGASPASP3AA684 - 694374 - 384
2272ARGARGASPASP3BB684 - 694374 - 384
3272ARGARGASPASP3CC684 - 694374 - 384
4272ARGARGASPASP3DD684 - 694374 - 384
5272ARGARGASPASP3EE684 - 694374 - 384
6272ARGARGASPASP3FF684 - 694374 - 384
1282ILEILEILEILE3AA704394
2282ILEILEILEILE3BB704394
3282ILEILEILEILE3CC704394
4282ILEILEILEILE3DD704394
5282ILEILEILEILE3EE704394
6282ILEILEILEILE3FF704394
1292VALVALVALVAL3AA708398
2292VALVALVALVAL3BB708398
3292VALVALVALVAL3CC708398
4292VALVALVALVAL3DD708398
5292VALVALVALVAL3EE708398
6292VALVALVALVAL3FF708398
1302GLUGLUILEILE3AA716 - 728406 - 418
2302GLUGLUILEILE3BB716 - 728406 - 418
3302GLUGLUILEILE3CC716 - 728406 - 418
4302GLUGLUILEILE3DD716 - 728406 - 418
5302GLUGLUILEILE3EE716 - 728406 - 418
6302GLUGLUILEILE3FF716 - 728406 - 418
1312ARGARGARGARG3AA730 - 735420 - 425
2312ARGARGARGARG3BB730 - 735420 - 425
3312ARGARGARGARG3CC730 - 735420 - 425
4312ARGARGARGARG3DD730 - 735420 - 425
5312ARGARGARGARG3EE730 - 735420 - 425
6312ARGARGARGARG3FF730 - 735420 - 425
1322SO4SO4SO4SO43AJ - N741 - 745
2322SO4SO4SO4SO43D - BFA - V741 - 745
3322SO4SO4SO4SO43B - CW - DA741 - 745
4322SO4SO4SO4SO43C - DEA - MA741 - 745
5322SO4SO4SO4SO43F - EUA - TA741 - 745
6322SO4SO4SO4SO43A - FJ - BB741 - 745

NCS ensembles :
ID
1
2

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / CODH/ACS / Acetyl-CoA synthase subunit / ACS subunit


Mass: 47781.617 Da / Num. of mol.: 6 / Fragment: truncated domain, residues 311-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: acsB2 / Plasmid: pLHK07 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase

-
Non-polymers , 6 types, 237 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2S
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.008 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 12, 2004
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 78758 / Num. obs: 78342 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 51.823 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.3 / Num. measured obs: 55207 / Num. unique all: 7323 / Num. unique obs: 14222 / % possible all: 99.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Xnemodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAO: ACS domain 2 (320-470) and domain 3 (500-729)
Resolution: 3→19.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.88 / SU B: 28.231 / SU ML: 0.241 / SU R Cruickshank DPI: 0.289 / SU Rfree: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: use of 12 TLS bodies and tight ncs restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3902 5 %RANDOM
Rwork0.171 ---
all0.173 78758 --
obs0.173 78314 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.04 Å2 / Biso mean: 57.237 Å2 / Biso min: 20.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å2-0.92 Å20 Å2
2---1.83 Å20 Å2
3---2.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å-
Luzzati d res low-3 Å
Luzzati sigma a0.24 Å-
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19742 0 216 189 20147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02220402
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.00927560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31652522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52224.097908
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.452153546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.87315138
X-RAY DIFFRACTIONr_chiral_restr0.1060.22978
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215268
X-RAY DIFFRACTIONr_nbd_refined0.2260.29395
X-RAY DIFFRACTIONr_nbtor_refined0.320.213974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2786
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.23
X-RAY DIFFRACTIONr_mcbond_it0.3691.512798
X-RAY DIFFRACTIONr_mcangle_it0.597220254
X-RAY DIFFRACTIONr_scbond_it1.0738474
X-RAY DIFFRACTIONr_scangle_it1.7344.57233
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2718TIGHT POSITIONAL0.10.1
12B2718TIGHT POSITIONAL0.090.1
13C2718TIGHT POSITIONAL0.10.1
14D2718TIGHT POSITIONAL0.10.1
15E2718TIGHT POSITIONAL0.090.1
16F2718TIGHT POSITIONAL0.10.1
11A2718TIGHT THERMAL0.381.5
12B2718TIGHT THERMAL0.361.5
13C2718TIGHT THERMAL0.351.5
14D2718TIGHT THERMAL0.421.5
15E2718TIGHT THERMAL0.411.5
16F2718TIGHT THERMAL0.351.5
21A308TIGHT POSITIONAL0.130.1
22B308TIGHT POSITIONAL0.120.1
23C308TIGHT POSITIONAL0.140.1
24D308TIGHT POSITIONAL0.10.1
25E308TIGHT POSITIONAL0.120.1
26F308TIGHT POSITIONAL0.120.1
21A346LOOSE POSITIONAL0.55
22B346LOOSE POSITIONAL0.545
23C346LOOSE POSITIONAL0.65
24D346LOOSE POSITIONAL0.495
25E346LOOSE POSITIONAL0.465
26F346LOOSE POSITIONAL0.495
21A308TIGHT THERMAL0.381.5
22B308TIGHT THERMAL0.291.5
23C308TIGHT THERMAL0.321.5
24D308TIGHT THERMAL0.361.5
25E308TIGHT THERMAL0.321.5
26F308TIGHT THERMAL0.311.5
21A346LOOSE THERMAL1.6410
22B346LOOSE THERMAL2.1110
23C346LOOSE THERMAL2.0410
24D346LOOSE THERMAL2.0610
25E346LOOSE THERMAL1.9510
26F346LOOSE THERMAL1.9510
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 285 -
Rwork0.248 5379 -
all-5664 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.5164-0.47670.56772.1299-0.64211.23290.0311-0.62920.15750.6938-0.26-0.392-0.18970.1780.22890.0417-0.1005-0.142-0.09250.0114-0.2502104.9511-5.237852.786
21.88270.6969-0.68862.5446-0.49961.7036-0.21870.7833-0.1509-1.07210.1131-0.25060.3874-0.10090.10550.33510.05140.12710.0144-0.0518-0.340794.5496-5.0734-15.6336
31.3215-0.061-0.13261.6481-1.25582.16170.02280.049-0.2842-0.3821-0.5127-0.85650.33860.52820.4899-0.10760.27930.2471-0.09530.36250.5237132.078-22.598519.0291
42.72330.04820.30761.7288-0.38871.32160.0319-0.1961-0.45910.1254-0.09480.11790.3632-0.12480.0629-0.1648-0.04380.031-0.372-0.0419-0.280779.4508-27.476731.4016
52.14290.5277-0.93211.8454-0.55281.47160.14350.28530.5235-0.11880.00670.4459-0.2768-0.301-0.1502-0.20830.12460.0132-0.3154-0.0057-0.167974.275214.721212.5806
61.6658-0.04410.15521.9864-1.07531.8818-0.00930.11550.11980.0373-0.3829-0.8928-0.12650.50020.3922-0.1990.02290.1374-0.12260.3380.3098128.384915.83358.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A317 - 737
2X-RAY DIFFRACTION1A738 - 745
3X-RAY DIFFRACTION2B317 - 736
4X-RAY DIFFRACTION2B738 - 745
5X-RAY DIFFRACTION3C317 - 736
6X-RAY DIFFRACTION3C738 - 745
7X-RAY DIFFRACTION4D317 - 737
8X-RAY DIFFRACTION4D738 - 745
9X-RAY DIFFRACTION5E317 - 736
10X-RAY DIFFRACTION5E738 - 745
11X-RAY DIFFRACTION6F317 - 736
12X-RAY DIFFRACTION6F738 - 745

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more