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

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基本情報

登録情報
データベース: PDB / ID: 5xmj
タイトルCrystal structure of quinol:fumarate reductase from Desulfovibrio gigas
要素
  • (fumarate reductase ...) x 2
  • Succinate dehydrogenase iron-sulfur subunit
キーワードELECTRON TRANSPORT / membrane protein / electron transfer / QFR / proton transfer
機能・相同性
機能・相同性情報


fumarate reductase (quinol) / : / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 ...fumarate reductase (quinol) / : / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / metal ion binding / plasma membrane
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
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
類似検索 - 構成要素
生物種Desulfovibrio gigas (バクテリア)
Desulfovibrio gigas DSM 1382 = ATCC 19364 (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.6 Å
データ登録者Guan, H.H. / Hsieh, Y.C. / Lin, P.R. / Chen, C.J.
資金援助 台湾, 1件
組織認可番号国
National Science Council105-2311-B-231-001-MY3 台湾
引用ジャーナル: Sci Rep / 年: 2018
タイトル: Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas.
著者: 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.
履歴
登録2017年5月15日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年6月6日Provider: repository / タイプ: Initial release
改定 1.12018年12月19日Group: Data collection / Database references / カテゴリ: 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
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
カテゴリ: 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
改定 2.12023年11月22日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)506,26343
ポリマ－492,76212
非ポリマー13,50231
水00
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)253,96723
ポリマ－246,3816
非ポリマー7,58617
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area35960 Å2
ΔGint-304 kcal/mol
Surface area74220 Å2
手法PISA
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)252,29620
ポリマ－246,3816
非ポリマー5,91614
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area33250 Å2
ΔGint-313 kcal/mol
Surface area73920 Å2
手法PISA
単位格子
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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
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ドメイン領域:
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アンサンブル:
ID
1
2
3

-
要素

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Fumarate reductase ... , 2種, 8分子 AEIMCGKO

#1: タンパク質
fumarate reductase flavoprotein subunit / FAD-binding protein


分子量: 68755.148 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Desulfovibrio gigas (バクテリア) / 参照: UniProt: T2GB49*PLUS
#3: タンパク質
fumarate reductase respiratory complex / membrane-embedded protein


分子量: 24734.865 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Desulfovibrio gigas (バクテリア) / 参照: UniProt: T2GAT5*PLUS

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タンパク質 / 糖 , 2種, 6分子 BFJN

#10: 糖 ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM
#2: タンパク質
Succinate dehydrogenase iron-sulfur subunit


分子量: 29700.373 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Desulfovibrio gigas DSM 1382 = ATCC 19364 (バクテリア)
参照: UniProt: T2G9X8*PLUS, succinate dehydrogenase

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非ポリマー , 7種, 29分子

#4: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / コメント: FAD*YM
#5: 化合物
ChemComp-FUM / FUMARIC ACID / 2-ブテン二酸


分子量: 116.072 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C4H4O4
#6: 化合物
ChemComp-F3S / FE3-S4 CLUSTER


分子量: 295.795 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe3S4
#7: 化合物
ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe4S4
#8: 化合物
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe2S2
#9: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#11: 化合物 ChemComp-MQ7 / MENAQUINONE-7 / メナキノン7


分子量: 648.999 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C46H64O2

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.02 Å3/Da / 溶媒含有率: 59.21 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 0.1% DDM, 100 mM NaCl, 28% PEG 8000, Tris buffer, 100 mM, pH 8.5, 291K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SPring-8 / ビームライン: BL44XU / 波長: 0.9 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2013年10月24日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9 Å / 相対比: 1
反射解像度: 3.6→29.804 Å / Num. obs: 64730 / % possible obs: 98 % / 冗長度: 10.1 % / Net I/σ(I): 10.1
反射 シェル解像度: 3.6→3.728 Å

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
SCALEPACKデータスケーリング
PDB_EXTRACT3.22データ抽出
HKL-2000データ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2BS2

2bs2


解像度: 3.6→29.804 Å / SU ML: 0.65 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 35.33 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3126 3233 5 %
Rwork0.2317 61466 -
obs0.2358 64699 98.26 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 555.6 Å2 / Biso mean: 97.8981 Å2 / Biso min: 20 Å2
精密化ステップサイクル: final / 解像度: 3.6→29.804 Å
タンパク質核酸リガンド溶媒全体
原子数33360 0 758 0 34118
Biso mean--88.55 --
残基数----4296
拘束条件
Refine-IDタイプDev ideal数
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-ID数Refine-IDRmsタイプ
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精密化 シェル

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

解像度 (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

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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