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- PDB-5xmj: Crystal structure of quinol:fumarate reductase from Desulfovibrio... -

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Basic information

Entry
Database: PDB / ID: 5xmj
TitleCrystal structure of quinol:fumarate reductase from Desulfovibrio gigas
Components
  • (fumarate reductase ...) x 2
  • Succinate dehydrogenase iron-sulfur subunit
KeywordsELECTRON TRANSPORT / membrane protein / electron transfer / QFR / proton transfer
Function / homology
Function and homology information


fumarate reductase (quinol) / : / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...fumarate reductase (quinol) / : / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. ...Fumarate reductase type B, transmembrane subunit / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 / IRON/SULFUR CLUSTER / Fumarate reductase iron-sulfur subunit / Fumarate reductase cytochrome b subunit / Putative fumarate reductase flavoprotein subunit
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
Desulfovibrio gigas DSM 1382 = ATCC 19364 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsGuan, H.H. / Hsieh, Y.C. / Lin, P.R. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council105-2311-B-231-001-MY3 Taiwan
CitationJournal: Sci Rep / Year: 2018
Title: Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas.
Authors: Guan, H.H. / Hsieh, Y.C. / Lin, P.J. / Huang, Y.C. / Yoshimura, M. / Chen, L.Y. / Chen, S.K. / Chuankhayan, P. / Lin, C.C. / Chen, N.C. / Nakagawa, A. / Chan, S.I. / Chen, C.J.
History
DepositionMay 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fumarate reductase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur subunit
C: fumarate reductase respiratory complex
E: fumarate reductase flavoprotein subunit
F: Succinate dehydrogenase iron-sulfur subunit
G: fumarate reductase respiratory complex
I: fumarate reductase flavoprotein subunit
J: Succinate dehydrogenase iron-sulfur subunit
K: fumarate reductase respiratory complex
M: fumarate reductase flavoprotein subunit
N: Succinate dehydrogenase iron-sulfur subunit
O: fumarate reductase respiratory complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)506,26343
Polymers492,76212
Non-polymers13,50231
Water0
1
A: fumarate reductase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur subunit
C: fumarate reductase respiratory complex
M: fumarate reductase flavoprotein subunit
N: Succinate dehydrogenase iron-sulfur subunit
O: fumarate reductase respiratory complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,96723
Polymers246,3816
Non-polymers7,58617
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35960 Å2
ΔGint-304 kcal/mol
Surface area74220 Å2
MethodPISA
2
E: fumarate reductase flavoprotein subunit
F: Succinate dehydrogenase iron-sulfur subunit
G: fumarate reductase respiratory complex
I: fumarate reductase flavoprotein subunit
J: Succinate dehydrogenase iron-sulfur subunit
K: fumarate reductase respiratory complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,29620
Polymers246,3816
Non-polymers5,91614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33250 Å2
ΔGint-313 kcal/mol
Surface area73920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.136, 131.772, 195.428
Angle α, β, γ (deg.)90.000, 94.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resseq 1:3 or resseq 5:17 or resseq...
21(chain F and (resseq 1:3 or resseq 5:17 or resseq...
31(chain J and (resseq 1:3 or resseq 5:17 or resseq...
41(chain N and (resseq 1:3 or resseq 5:17 or resseq...
12(chain A and (resseq 1:29 or resseq 31:58 or resseq...
22(chain E and (resseq 1:29 or resseq 31:58 or resseq...
32(chain I and (resseq 1:29 or resseq 31:58 or resseq...
42(chain M and (resseq 1:29 or resseq 31:58 or resseq...
13(chain C and (resseq 1:5 or resseq 7:8 or resseq...
23(chain G and (resseq 1:5 or resseq 7:8 or resseq...
33(chain K and (resseq 1:5 or resseq 7:8 or resseq...
43(chain O and (resseq 1:5 or resseq 7:8 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETARGARG(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB1 - 31 - 3
121LEULEUPROPRO(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB5 - 175 - 17
131SERSERGLNGLN(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB19 - 2019 - 20
141PROPROPROPRO(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB2121
151METMETVALVAL(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB1 - 2401 - 240
161METMETVALVAL(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB1 - 2401 - 240
171METMETVALVAL(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB1 - 2401 - 240
181METMETVALVAL(chain B and (resseq 1:3 or resseq 5:17 or resseq...BB1 - 2401 - 240
211METMETARGARG(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE1 - 31 - 3
221LEULEUPROPRO(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE5 - 175 - 17
231SERSERGLNGLN(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE19 - 2019 - 20
241PROPROPROPRO(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE2121
251METMETVALVAL(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE1 - 2401 - 240
261METMETVALVAL(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE1 - 2401 - 240
271METMETVALVAL(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE1 - 2401 - 240
281METMETVALVAL(chain F and (resseq 1:3 or resseq 5:17 or resseq...FE1 - 2401 - 240
311METMETARGARG(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH1 - 31 - 3
321LEULEUPROPRO(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH5 - 175 - 17
331SERSERGLNGLN(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH19 - 2019 - 20
341PROPROPROPRO(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH2121
351METMETVALVAL(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH1 - 2401 - 240
361METMETVALVAL(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH1 - 2401 - 240
371METMETVALVAL(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH1 - 2401 - 240
381METMETVALVAL(chain J and (resseq 1:3 or resseq 5:17 or resseq...JH1 - 2401 - 240
411METMETARGARG(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK1 - 31 - 3
421LEULEUPROPRO(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK5 - 175 - 17
431SERSERGLNGLN(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK19 - 2019 - 20
441PROPROPROPRO(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK2121
451METMETVALVAL(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK1 - 2401 - 240
461METMETVALVAL(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK1 - 2401 - 240
471METMETVALVAL(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK1 - 2401 - 240
481METMETVALVAL(chain N and (resseq 1:3 or resseq 5:17 or resseq...NK1 - 2401 - 240
112METMETLEULEU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA1 - 291 - 29
122THRTHRALAALA(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA31 - 5831 - 58
132GLYGLYVALVAL(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA61 - 7461 - 74
142GLYGLYASPASP(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA76 - 7876 - 78
152GLYGLYALAALA(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA80 - 10180 - 101
162TRPTRPTHRTHR(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA103 - 116103 - 116
172TYRTYRGLYGLY(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA118 - 121118 - 121
182PROPROPROPRO(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA123123
192ALAALAGLUGLU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA126 - 127126 - 127
1102LYSLYSALAALA(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA129 - 138129 - 138
1112ALAALAASNASN(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA140 - 250140 - 250
1122GLUGLUCYSCYS(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA252 - 272252 - 272
1132GLYGLYGLYGLY(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA276276
1142THRTHRLEULEU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA278 - 279278 - 279
1152VALVALGLNGLN(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA282 - 284282 - 284
1162ARGARGPHEPHE(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA286 - 287286 - 287
1172PROPROASPASP(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA289 - 294289 - 294
1182LEULEUSERSER(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA298 - 305298 - 305
1192METMETMETMET(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA308 - 312308 - 312
1202LYSLYSGLYGLY(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA314 - 315314 - 315
1212GLYGLYVALVAL(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA317 - 318317 - 318
1222SERSERSERSER(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA320320
1232METMETLEULEU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA1 - 6221 - 622
1242METMETLEULEU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA1 - 6221 - 622
1252METMETLEULEU(chain A and (resseq 1:29 or resseq 31:58 or resseq...AA1 - 6221 - 622
212METMETLEULEU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED1 - 291 - 29
222THRTHRALAALA(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED31 - 5831 - 58
232GLYGLYVALVAL(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED61 - 7461 - 74
242GLYGLYASPASP(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED76 - 7876 - 78
252GLYGLYALAALA(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED80 - 10180 - 101
262TRPTRPTHRTHR(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED103 - 116103 - 116
272TYRTYRGLYGLY(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED118 - 121118 - 121
282PROPROPROPRO(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED123123
292ALAALAGLUGLU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED126 - 127126 - 127
2102LYSLYSALAALA(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED129 - 138129 - 138
2112ALAALAASNASN(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED140 - 250140 - 250
2122GLUGLUCYSCYS(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED252 - 272252 - 272
2132GLYGLYGLYGLY(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED276276
2142THRTHRLEULEU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED278 - 279278 - 279
2152VALVALGLNGLN(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED282 - 284282 - 284
2162ARGARGPHEPHE(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED286 - 287286 - 287
2172PROPROASPASP(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED289 - 294289 - 294
2182LEULEUSERSER(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED298 - 305298 - 305
2192METMETMETMET(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED308 - 312308 - 312
2202LYSLYSGLYGLY(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED314 - 315314 - 315
2212GLYGLYVALVAL(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED317 - 318317 - 318
2222SERSERSERSER(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED320320
2232METMETLEULEU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED1 - 6221 - 622
2242METMETLEULEU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED1 - 6221 - 622
2252METMETLEULEU(chain E and (resseq 1:29 or resseq 31:58 or resseq...ED1 - 6221 - 622
312METMETLEULEU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG1 - 291 - 29
322THRTHRALAALA(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG31 - 5831 - 58
332GLYGLYVALVAL(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG61 - 7461 - 74
342GLYGLYASPASP(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG76 - 7876 - 78
352GLYGLYALAALA(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG80 - 10180 - 101
362TRPTRPTHRTHR(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG103 - 116103 - 116
372TYRTYRGLYGLY(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG118 - 121118 - 121
382PROPROPROPRO(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG123123
392ALAALAGLUGLU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG126 - 127126 - 127
3102LYSLYSALAALA(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG129 - 138129 - 138
3112ALAALAASNASN(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG140 - 250140 - 250
3122GLUGLUCYSCYS(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG252 - 272252 - 272
3132GLYGLYGLYGLY(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG276276
3142THRTHRLEULEU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG278 - 279278 - 279
3152VALVALGLNGLN(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG282 - 284282 - 284
3162ARGARGPHEPHE(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG286 - 287286 - 287
3172PROPROASPASP(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG289 - 294289 - 294
3182LEULEUSERSER(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG298 - 305298 - 305
3192METMETMETMET(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG308 - 312308 - 312
3202LYSLYSGLYGLY(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG314 - 315314 - 315
3212GLYGLYVALVAL(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG317 - 318317 - 318
3222SERSERSERSER(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG320320
3232METMETLEULEU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG1 - 6221 - 622
3242METMETLEULEU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG1 - 6221 - 622
3252METMETLEULEU(chain I and (resseq 1:29 or resseq 31:58 or resseq...IG1 - 6221 - 622
412METMETLEULEU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ1 - 291 - 29
422THRTHRALAALA(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ31 - 5831 - 58
432GLYGLYVALVAL(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ61 - 7461 - 74
442GLYGLYASPASP(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ76 - 7876 - 78
452GLYGLYALAALA(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ80 - 10180 - 101
462TRPTRPTHRTHR(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ103 - 116103 - 116
472TYRTYRGLYGLY(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ118 - 121118 - 121
482PROPROPROPRO(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ123123
492ALAALAGLUGLU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ126 - 127126 - 127
4102LYSLYSALAALA(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ129 - 138129 - 138
4112ALAALAASNASN(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ140 - 250140 - 250
4122GLUGLUCYSCYS(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ252 - 272252 - 272
4132GLYGLYGLYGLY(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ276276
4142THRTHRLEULEU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ278 - 279278 - 279
4152VALVALGLNGLN(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ282 - 284282 - 284
4162ARGARGPHEPHE(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ286 - 287286 - 287
4172PROPROASPASP(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ289 - 294289 - 294
4182LEULEUSERSER(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ298 - 305298 - 305
4192METMETMETMET(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ308 - 312308 - 312
4202LYSLYSGLYGLY(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ314 - 315314 - 315
4212GLYGLYVALVAL(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ317 - 318317 - 318
4222SERSERSERSER(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ320320
4232METMETLEULEU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ1 - 6221 - 622
4242METMETLEULEU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ1 - 6221 - 622
4252METMETLEULEU(chain M and (resseq 1:29 or resseq 31:58 or resseq...MJ1 - 6221 - 622
113METMETTHRTHR(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1 - 51 - 5
123THRTHRLEULEU(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC7 - 87 - 8
133PROPROGLNGLN(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC11 - 1211 - 12
143SERSERSERSER(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1414
153ILEILEPHEPHE(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC16 - 2216 - 22
163GLNGLNLEULEU(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC24 - 3524 - 35
173ALAALASERSER(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC37 - 4437 - 44
183VALVALVALVAL(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC4545
193METMETMETMET(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1 - 2121 - 212
1103METMETMETMET(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1 - 2121 - 212
1113METMETMETMET(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1 - 2121 - 212
1123METMETMETMET(chain C and (resseq 1:5 or resseq 7:8 or resseq...CC1 - 2121 - 212
213METMETTHRTHR(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1 - 51 - 5
223THRTHRLEULEU(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF7 - 87 - 8
233PROPROGLNGLN(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF11 - 1211 - 12
243SERSERSERSER(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1414
253ILEILEPHEPHE(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF16 - 2216 - 22
263GLNGLNLEULEU(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF24 - 3524 - 35
273ALAALASERSER(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF37 - 4437 - 44
283VALVALVALVAL(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF4545
293METMETMETMET(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1 - 2121 - 212
2103METMETMETMET(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1 - 2121 - 212
2113METMETMETMET(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1 - 2121 - 212
2123METMETMETMET(chain G and (resseq 1:5 or resseq 7:8 or resseq...GF1 - 2121 - 212
313METMETTHRTHR(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1 - 51 - 5
323THRTHRLEULEU(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI7 - 87 - 8
333PROPROGLNGLN(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI11 - 1211 - 12
343SERSERSERSER(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1414
353ILEILEPHEPHE(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI16 - 2216 - 22
363GLNGLNLEULEU(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI24 - 3524 - 35
373ALAALASERSER(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI37 - 4437 - 44
383VALVALVALVAL(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI4545
393METMETMETMET(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1 - 2121 - 212
3103METMETMETMET(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1 - 2121 - 212
3113METMETMETMET(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1 - 2121 - 212
3123METMETMETMET(chain K and (resseq 1:5 or resseq 7:8 or resseq...KI1 - 2121 - 212
413METMETTHRTHR(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1 - 51 - 5
423THRTHRLEULEU(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL7 - 87 - 8
433PROPROGLNGLN(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL11 - 1211 - 12
443SERSERSERSER(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1414
453ILEILEPHEPHE(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL16 - 2216 - 22
463GLNGLNLEULEU(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL24 - 3524 - 35
473ALAALASERSER(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL37 - 4437 - 44
483VALVALVALVAL(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL4545
493METMETMETMET(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1 - 2121 - 212
4103METMETMETMET(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1 - 2121 - 212
4113METMETMETMET(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1 - 2121 - 212
4123METMETMETMET(chain O and (resseq 1:5 or resseq 7:8 or resseq...OL1 - 2121 - 212

NCS ensembles :
ID
1
2
3

-
Components

-
Fumarate reductase ... , 2 types, 8 molecules AEIMCGKO

#1: Protein
fumarate reductase flavoprotein subunit / FAD-binding protein


Mass: 68755.148 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: T2GB49*PLUS
#3: Protein
fumarate reductase respiratory complex / membrane-embedded protein


Mass: 24734.865 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: T2GAT5*PLUS

-
Protein / Sugars , 2 types, 6 molecules BFJN

#10: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#2: Protein
Succinate dehydrogenase iron-sulfur subunit


Mass: 29700.373 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio gigas DSM 1382 = ATCC 19364 (bacteria)
References: UniProt: T2G9X8*PLUS, succinate dehydrogenase

-
Non-polymers , 7 types, 29 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4
#6: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1% DDM, 100 mM NaCl, 28% PEG 8000, Tris buffer, 100 mM, pH 8.5, 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.6→29.804 Å / Num. obs: 64730 / % possible obs: 98 % / Redundancy: 10.1 % / Net I/σ(I): 10.1
Reflection shellResolution: 3.6→3.728 Å

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BS2

2bs2


Resolution: 3.6→29.804 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3126 3233 5 %
Rwork0.2317 61466 -
obs0.2358 64699 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 555.6 Å2 / Biso mean: 97.8981 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.6→29.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33360 0 758 0 34118
Biso mean--88.55 --
Num. residues----4296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01535002
X-RAY DIFFRACTIONf_angle_d1.79147403
X-RAY DIFFRACTIONf_chiral_restr0.0845121
X-RAY DIFFRACTIONf_plane_restr0.016018
X-RAY DIFFRACTIONf_dihedral_angle_d15.02820504
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B4000X-RAY DIFFRACTION10.92TORSIONAL
12F4000X-RAY DIFFRACTION10.92TORSIONAL
13J4000X-RAY DIFFRACTION10.92TORSIONAL
24N4000X-RAY DIFFRACTION10.92TORSIONAL
21A9448X-RAY DIFFRACTION10.92TORSIONAL
22E9448X-RAY DIFFRACTION10.92TORSIONAL
23I9448X-RAY DIFFRACTION10.92TORSIONAL
24M9448X-RAY DIFFRACTION10.92TORSIONAL
31C2815X-RAY DIFFRACTION10.92TORSIONAL
32G2815X-RAY DIFFRACTION10.92TORSIONAL
33K2815X-RAY DIFFRACTION10.92TORSIONAL
34O2815X-RAY DIFFRACTION10.92TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6001-3.65370.43661370.36322677281499
3.6537-3.71070.39941410.34352683282499
3.7107-3.77140.36891500.32562716286699
3.7714-3.83630.43221360.313426662802100
3.8363-3.90590.39321560.31062664282099
3.9059-3.98090.34641150.29572740285599
3.9809-4.06190.43191470.29422673282099
4.0619-4.150.37791420.28272711285399
4.15-4.24630.32881350.274326762811100
4.2463-4.35220.32771440.242726932837100
4.3522-4.46950.32281500.240227102860100
4.4695-4.60050.31461520.222426602812100
4.6005-4.74850.33541440.221327222866100
4.7485-4.91750.30341330.223227082841100
4.9175-5.11340.38071400.212827332873100
5.1134-5.34490.33711280.221927172845100
5.3449-5.62490.2981350.203427152850100
5.6249-5.97470.32061680.215526912859100
5.9747-6.43170.30291380.20862693283199
6.4317-7.07110.30391340.20272718285299
7.0711-8.07650.29691570.17372662281997
8.0765-10.10910.21621310.17422450258189
10.1091-29.80530.27571200.23552388250885

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