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- PDB-7npa: Crystal structure of the Coenzyme F420-dependent sulfite reductas... -

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基本情報

登録情報
データベース: PDB / ID: 7npa
タイトルCrystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution
要素Coenzyme F420-dependent sulfite reductase
キーワードOXIDOREDUCTASE (酸化還元酵素) / Sulfite detoxification / Sulfur metabolism / sulfide (硫化物) / hydrogenotrophic methanogens / iron-sulfur cluster (鉄・硫黄クラスター) / sulfite-reductase evolution / sulfite/nitrite reductase / siroheme (シロヘム) / flavin / ferredoxin (フェレドキシン) / F420 / thermophile (好熱菌)
機能・相同性
機能・相同性情報


4 iron, 4 sulfur cluster binding / oxidoreductase activity / heme binding / metal ion binding
類似検索 - 分子機能
Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily ...Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 4Fe-4S binding domain / 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
類似検索 - ドメイン・相同性
フラビンアデニンジヌクレオチド / 硫化水素 / : / DI(HYDROXYETHYL)ETHER / 鉄・硫黄クラスター / シロヘム / Coenzyme F420-dependent sulfite reductase
類似検索 - 構成要素
生物種Methanothermococcus thermolithotrophicus DSM 2095 (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.55 Å
データ登録者Jespersen, M. / Wagner, T.
資金援助 ドイツ, 2件
組織認可番号国
Max Planck Society/ ドイツ
German Research Foundation (DFG)Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1 ドイツ
引用
ジャーナル: Nat.Chem.Biol. / 年: 2023
タイトル: Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.
著者: Jespersen, M. / Pierik, A.J. / Wagner, T.
#1: ジャーナル: Biorxiv / 年: 2022
タイトル: The structure of the F420-dependent sulfite-detoxifying enzyme from Methanococcales reveals a prototypical sulfite-reductase with assimilatory traits
著者: Jespersen, M. / Pierik, A.J. / Wagner, T.
履歴
登録2021年2月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年3月23日Provider: repository / タイプ: Initial release
改定 1.12023年4月5日Group: Database references / Refinement description
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y ..._pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.selection_details
改定 2.02023年12月6日Group: Data collection / Non-polymer description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
改定 2.12024年2月7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

ダウンロードとリンク

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集合体

登録構造単位
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
E: Coenzyme F420-dependent sulfite reductase
F: Coenzyme F420-dependent sulfite reductase
G: Coenzyme F420-dependent sulfite reductase
H: Coenzyme F420-dependent sulfite reductase
I: Coenzyme F420-dependent sulfite reductase
J: Coenzyme F420-dependent sulfite reductase
K: Coenzyme F420-dependent sulfite reductase
L: Coenzyme F420-dependent sulfite reductase
M: Coenzyme F420-dependent sulfite reductase
N: Coenzyme F420-dependent sulfite reductase
O: Coenzyme F420-dependent sulfite reductase
P: Coenzyme F420-dependent sulfite reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,184,791375
ポリマ－1,107,92316
非ポリマー76,868359
水194,05810772
1
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)296,378102
ポリマ－276,9814
非ポリマー19,39798
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area47340 Å2
ΔGint-691 kcal/mol
Surface area90310 Å2
手法PISA
2
E: Coenzyme F420-dependent sulfite reductase
F: Coenzyme F420-dependent sulfite reductase
G: Coenzyme F420-dependent sulfite reductase
H: Coenzyme F420-dependent sulfite reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)295,58789
ポリマ－276,9814
非ポリマー18,60785
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area45540 Å2
ΔGint-740 kcal/mol
Surface area90570 Å2
手法PISA
3
I: Coenzyme F420-dependent sulfite reductase
J: Coenzyme F420-dependent sulfite reductase
K: Coenzyme F420-dependent sulfite reductase
L: Coenzyme F420-dependent sulfite reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)295,69189
ポリマ－276,9814
非ポリマー18,71185
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area45260 Å2
ΔGint-743 kcal/mol
Surface area90380 Å2
手法PISA
4
M: Coenzyme F420-dependent sulfite reductase
N: Coenzyme F420-dependent sulfite reductase
O: Coenzyme F420-dependent sulfite reductase
P: Coenzyme F420-dependent sulfite reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)297,13595
ポリマ－276,9814
非ポリマー20,15491
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area46550 Å2
ΔGint-764 kcal/mol
Surface area90720 Å2
手法PISA
単位格子
Length a, b, c (Å)113.148, 124.157, 241.062
Angle α, β, γ (deg.)102.280, 95.710, 90.250
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 4 or resid 6...
21(chain B and (resid 2 through 4 or resid 6...
31(chain C and (resid 2 through 4 or resid 6...
41(chain D and (resid 2 through 4 or resid 6...
51(chain E and (resid 2 through 4 or resid 6...
61(chain F and (resid 2 through 4 or resid 6...
71(chain G and (resid 2 through 4 or resid 6...
81(chain H and (resid 2 through 4 or resid 6...
91(chain I and (resid 2 through 4 or resid 6...
101(chain J and (resid 2 through 4 or resid 6...
111(chain K and (resid 2 through 4 or resid 6...
121(chain L and (resid 2 through 4 or resid 6...
131(chain M and (resid 2 through 4 or resid 6...
141(chain N and (resid 2 through 4 or resid 6...
151(chain O and (resid 2 through 4 or resid 6...
161(chain P and (resid 2 through 4 or resid 6...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 4 or resid 6...A2 - 4
121(chain A and (resid 2 through 4 or resid 6...A6 - 60
131(chain A and (resid 2 through 4 or resid 6...A62 - 70
141(chain A and (resid 2 through 4 or resid 6...A452
151(chain A and (resid 2 through 4 or resid 6...A1 - 618
161(chain A and (resid 2 through 4 or resid 6...A6 - 510
171(chain A and (resid 2 through 4 or resid 6...A512 - 514
181(chain A and (resid 2 through 4 or resid 6...A530 - 568
191(chain A and (resid 2 through 4 or resid 6...A613 - 611
1101(chain A and (resid 2 through 4 or resid 6...A613 - 618
1111(chain A and (resid 2 through 4 or resid 6...A1201 - 1601
211(chain B and (resid 2 through 4 or resid 6...B2 - 4
221(chain B and (resid 2 through 4 or resid 6...B6 - 60
231(chain B and (resid 2 through 4 or resid 6...B62 - 70
241(chain B and (resid 2 through 4 or resid 6...B1 - 618
251(chain B and (resid 2 through 4 or resid 6...B0
261(chain B and (resid 2 through 4 or resid 6...B454
271(chain B and (resid 2 through 4 or resid 6...B0
281(chain B and (resid 2 through 4 or resid 6...B1 - 618
291(chain B and (resid 2 through 4 or resid 6...B530 - 568
2101(chain B and (resid 2 through 4 or resid 6...B585 - 611
2111(chain B and (resid 2 through 4 or resid 6...B613 - 618
2121(chain B and (resid 2 through 4 or resid 6...B1201 - 1601
311(chain C and (resid 2 through 4 or resid 6...C2 - 4
321(chain C and (resid 2 through 4 or resid 6...C6 - 60
331(chain C and (resid 2 through 4 or resid 6...C62 - 70
341(chain C and (resid 2 through 4 or resid 6...C454
351(chain C and (resid 2 through 4 or resid 6...C452
361(chain C and (resid 2 through 4 or resid 6...C1 - 618
371(chain C and (resid 2 through 4 or resid 6...C1 - 618
381(chain C and (resid 2 through 4 or resid 6...C516 - 528
391(chain C and (resid 2 through 4 or resid 6...C530 - 568
3101(chain C and (resid 2 through 4 or resid 6...C613 - 611
3111(chain C and (resid 2 through 4 or resid 6...C613 - 618
3121(chain C and (resid 2 through 4 or resid 6...C1201 - 1601
411(chain D and (resid 2 through 4 or resid 6...D2 - 4
421(chain D and (resid 2 through 4 or resid 6...D6 - 60
431(chain D and (resid 2 through 4 or resid 6...D62 - 70
441(chain D and (resid 2 through 4 or resid 6...D452
451(chain D and (resid 2 through 4 or resid 6...D2 - 618
461(chain D and (resid 2 through 4 or resid 6...D6 - 510
471(chain D and (resid 2 through 4 or resid 6...D512 - 514
481(chain D and (resid 2 through 4 or resid 6...D530 - 568
491(chain D and (resid 2 through 4 or resid 6...D613 - 611
4101(chain D and (resid 2 through 4 or resid 6...D613 - 617
4111(chain D and (resid 2 through 4 or resid 6...D618
4121(chain D and (resid 2 through 4 or resid 6...D2 - 618
4131(chain D and (resid 2 through 4 or resid 6...D2 - 618
4141(chain D and (resid 2 through 4 or resid 6...D2 - 618
4151(chain D and (resid 2 through 4 or resid 6...D2 - 618
4161(chain D and (resid 2 through 4 or resid 6...D2 - 618
4171(chain D and (resid 2 through 4 or resid 6...D2 - 618
4181(chain D and (resid 2 through 4 or resid 6...D2 - 618
4191(chain D and (resid 2 through 4 or resid 6...D2 - 618
511(chain E and (resid 2 through 4 or resid 6...E2 - 4
521(chain E and (resid 2 through 4 or resid 6...E6 - 60
531(chain E and (resid 2 through 4 or resid 6...E62 - 70
541(chain E and (resid 2 through 4 or resid 6...E311
551(chain E and (resid 2 through 4 or resid 6...E337 - 452
561(chain E and (resid 2 through 4 or resid 6...E454
571(chain E and (resid 2 through 4 or resid 6...E456 - 510
581(chain E and (resid 2 through 4 or resid 6...E512 - 514
591(chain E and (resid 2 through 4 or resid 6...E516 - 528
5101(chain E and (resid 2 through 4 or resid 6...E530 - 568
5111(chain E and (resid 2 through 4 or resid 6...E570 - 583
5121(chain E and (resid 2 through 4 or resid 6...E585 - 611
5131(chain E and (resid 2 through 4 or resid 6...E613 - 618
5141(chain E and (resid 2 through 4 or resid 6...E1201 - 1601
611(chain F and (resid 2 through 4 or resid 6...F2 - 4
621(chain F and (resid 2 through 4 or resid 6...F6 - 60
631(chain F and (resid 2 through 4 or resid 6...F62 - 70
641(chain F and (resid 2 through 4 or resid 6...F311
651(chain F and (resid 2 through 4 or resid 6...F1 - 618
661(chain F and (resid 2 through 4 or resid 6...F1 - 618
671(chain F and (resid 2 through 4 or resid 6...F1 - 618
681(chain F and (resid 2 through 4 or resid 6...F1 - 618
691(chain F and (resid 2 through 4 or resid 6...F516 - 528
6101(chain F and (resid 2 through 4 or resid 6...F0
6111(chain F and (resid 2 through 4 or resid 6...F1 - 618
6121(chain F and (resid 2 through 4 or resid 6...F613 - 618
6131(chain F and (resid 2 through 4 or resid 6...F1201 - 8
6141(chain F and (resid 2 through 4 or resid 6...F1201 - 1601
711(chain G and (resid 2 through 4 or resid 6...G2 - 4
721(chain G and (resid 2 through 4 or resid 6...G6 - 60
731(chain G and (resid 2 through 4 or resid 6...G0
741(chain G and (resid 2 through 4 or resid 6...G452
751(chain G and (resid 2 through 4 or resid 6...G1 - 618
761(chain G and (resid 2 through 4 or resid 6...G6 - 510
771(chain G and (resid 2 through 4 or resid 6...G512 - 514
781(chain G and (resid 2 through 4 or resid 6...G530 - 568
791(chain G and (resid 2 through 4 or resid 6...G613 - 611
7101(chain G and (resid 2 through 4 or resid 6...G613 - 618
7111(chain G and (resid 2 through 4 or resid 6...G1201 - 1601
811(chain H and (resid 2 through 4 or resid 6...H2 - 4
821(chain H and (resid 2 through 4 or resid 6...H6 - 60
831(chain H and (resid 2 through 4 or resid 6...H62 - 70
841(chain H and (resid 2 through 4 or resid 6...H2 - 618
851(chain H and (resid 2 through 4 or resid 6...H0
861(chain H and (resid 2 through 4 or resid 6...H454
871(chain H and (resid 2 through 4 or resid 6...H0
881(chain H and (resid 2 through 4 or resid 6...H2 - 618
891(chain H and (resid 2 through 4 or resid 6...H530 - 568
8101(chain H and (resid 2 through 4 or resid 6...H585 - 611
8111(chain H and (resid 2 through 4 or resid 6...H613 - 618
8121(chain H and (resid 2 through 4 or resid 6...H1201 - 1601
911(chain I and (resid 2 through 4 or resid 6...I2 - 4
921(chain I and (resid 2 through 4 or resid 6...I6 - 60
931(chain I and (resid 2 through 4 or resid 6...I62 - 70
941(chain I and (resid 2 through 4 or resid 6...I311
951(chain I and (resid 2 through 4 or resid 6...I337 - 452
961(chain I and (resid 2 through 4 or resid 6...I454
971(chain I and (resid 2 through 4 or resid 6...I456 - 510
981(chain I and (resid 2 through 4 or resid 6...I512 - 514
991(chain I and (resid 2 through 4 or resid 6...I516 - 528
9101(chain I and (resid 2 through 4 or resid 6...I530 - 568
9111(chain I and (resid 2 through 4 or resid 6...I570 - 583
9121(chain I and (resid 2 through 4 or resid 6...I585 - 611
9131(chain I and (resid 2 through 4 or resid 6...I613 - 618
9141(chain I and (resid 2 through 4 or resid 6...I1201 - 1601
1011(chain J and (resid 2 through 4 or resid 6...J2 - 4
1021(chain J and (resid 2 through 4 or resid 6...J6 - 60
1031(chain J and (resid 2 through 4 or resid 6...J0
1041(chain J and (resid 2 through 4 or resid 6...J1 - 618
1051(chain J and (resid 2 through 4 or resid 6...J456 - 510
1061(chain J and (resid 2 through 4 or resid 6...J6 - 510
1071(chain J and (resid 2 through 4 or resid 6...J512 - 514
1081(chain J and (resid 2 through 4 or resid 6...J516 - 528
1091(chain J and (resid 2 through 4 or resid 6...J570 - 583
10101(chain J and (resid 2 through 4 or resid 6...J613 - 6
10111(chain J and (resid 2 through 4 or resid 6...J613 - 617
10121(chain J and (resid 2 through 4 or resid 6...J618
10131(chain J and (resid 2 through 4 or resid 6...J1 - 618
10141(chain J and (resid 2 through 4 or resid 6...J1 - 618
10151(chain J and (resid 2 through 4 or resid 6...J1 - 618
10161(chain J and (resid 2 through 4 or resid 6...J1 - 618
10171(chain J and (resid 2 through 4 or resid 6...J1 - 618
10181(chain J and (resid 2 through 4 or resid 6...J1 - 618
10191(chain J and (resid 2 through 4 or resid 6...J1 - 618
1111(chain K and (resid 2 through 4 or resid 6...K2 - 4
1121(chain K and (resid 2 through 4 or resid 6...K6 - 60
1131(chain K and (resid 2 through 4 or resid 6...K62 - 70
1141(chain K and (resid 2 through 4 or resid 6...K2 - 618
1151(chain K and (resid 2 through 4 or resid 6...K0
1161(chain K and (resid 2 through 4 or resid 6...K454
1171(chain K and (resid 2 through 4 or resid 6...K0
1181(chain K and (resid 2 through 4 or resid 6...K2 - 618
1191(chain K and (resid 2 through 4 or resid 6...K530 - 568
11101(chain K and (resid 2 through 4 or resid 6...K585 - 611
11111(chain K and (resid 2 through 4 or resid 6...K613 - 618
11121(chain K and (resid 2 through 4 or resid 6...K1201 - 1601
1211(chain L and (resid 2 through 4 or resid 6...L2 - 4
1221(chain L and (resid 2 through 4 or resid 6...L6 - 60
1231(chain L and (resid 2 through 4 or resid 6...L62 - 70
1241(chain L and (resid 2 through 4 or resid 6...L2 - 618
1251(chain L and (resid 2 through 4 or resid 6...L0
1261(chain L and (resid 2 through 4 or resid 6...L454
1271(chain L and (resid 2 through 4 or resid 6...L0
1281(chain L and (resid 2 through 4 or resid 6...L2 - 618
1291(chain L and (resid 2 through 4 or resid 6...L530 - 568
12101(chain L and (resid 2 through 4 or resid 6...L585 - 611
12111(chain L and (resid 2 through 4 or resid 6...L613 - 618
12121(chain L and (resid 2 through 4 or resid 6...L1201 - 1601
1311(chain M and (resid 2 through 4 or resid 6...M2 - 4
1321(chain M and (resid 2 through 4 or resid 6...M6 - 60
1331(chain M and (resid 2 through 4 or resid 6...M62 - 70
1341(chain M and (resid 2 through 4 or resid 6...M311
1351(chain M and (resid 2 through 4 or resid 6...M337 - 452
1361(chain M and (resid 2 through 4 or resid 6...M454
1371(chain M and (resid 2 through 4 or resid 6...M456 - 510
1381(chain M and (resid 2 through 4 or resid 6...M512 - 514
1391(chain M and (resid 2 through 4 or resid 6...M516 - 528
13101(chain M and (resid 2 through 4 or resid 6...M530 - 568
13111(chain M and (resid 2 through 4 or resid 6...M570 - 583
13121(chain M and (resid 2 through 4 or resid 6...M585 - 611
13131(chain M and (resid 2 through 4 or resid 6...M613 - 618
13141(chain M and (resid 2 through 4 or resid 6...M1201 - 1601
1411(chain N and (resid 2 through 4 or resid 6...N2 - 4
1421(chain N and (resid 2 through 4 or resid 6...N6 - 60
1431(chain N and (resid 2 through 4 or resid 6...N62 - 70
1441(chain N and (resid 2 through 4 or resid 6...N311
1451(chain N and (resid 2 through 4 or resid 6...N2 - 618
1461(chain N and (resid 2 through 4 or resid 6...N2 - 618
1471(chain N and (resid 2 through 4 or resid 6...N2 - 618
1481(chain N and (resid 2 through 4 or resid 6...N2 - 618
1491(chain N and (resid 2 through 4 or resid 6...N516 - 528
14101(chain N and (resid 2 through 4 or resid 6...N0
14111(chain N and (resid 2 through 4 or resid 6...N2 - 618
14121(chain N and (resid 2 through 4 or resid 6...N613 - 618
14131(chain N and (resid 2 through 4 or resid 6...N1201 - 8
14141(chain N and (resid 2 through 4 or resid 6...N1201 - 1601
1511(chain O and (resid 2 through 4 or resid 6...O2 - 4
1521(chain O and (resid 2 through 4 or resid 6...O6 - 60
1531(chain O and (resid 2 through 4 or resid 6...O0
1541(chain O and (resid 2 through 4 or resid 6...O452
1551(chain O and (resid 2 through 4 or resid 6...O2 - 618
1561(chain O and (resid 2 through 4 or resid 6...O6 - 510
1571(chain O and (resid 2 through 4 or resid 6...O512 - 514
1581(chain O and (resid 2 through 4 or resid 6...O530 - 568
1591(chain O and (resid 2 through 4 or resid 6...O613 - 611
15101(chain O and (resid 2 through 4 or resid 6...O613 - 618
15111(chain O and (resid 2 through 4 or resid 6...O1201 - 1601
1611(chain P and (resid 2 through 4 or resid 6...P2 - 4
1621(chain P and (resid 2 through 4 or resid 6...P6 - 60
1631(chain P and (resid 2 through 4 or resid 6...P62 - 70
1641(chain P and (resid 2 through 4 or resid 6...P2 - 618
1651(chain P and (resid 2 through 4 or resid 6...P0
1661(chain P and (resid 2 through 4 or resid 6...P454
1671(chain P and (resid 2 through 4 or resid 6...P0
1681(chain P and (resid 2 through 4 or resid 6...P2 - 618
1691(chain P and (resid 2 through 4 or resid 6...P530 - 568
16101(chain P and (resid 2 through 4 or resid 6...P585 - 611
16111(chain P and (resid 2 through 4 or resid 6...P613 - 618
16121(chain P and (resid 2 through 4 or resid 6...P1201 - 1601

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要素

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タンパク質 , 1種, 16分子 ABCDEFGHIJKLMNOP

#1: タンパク質
Coenzyme F420-dependent sulfite reductase


分子量: 69245.164 Da / 分子数: 16 / 変異: wild-type / 由来タイプ: 天然 / 詳細: /
由来: (天然) Methanothermococcus thermolithotrophicus DSM 2095 (古細菌)
細胞株: / / 器官: / / Plasmid details: / / Variant: / / 株: DSM 2095 / 組織: /
参照: UniProt: A0A2Z5PF12, sulfite reductase (coenzyme F420)

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非ポリマー , 12種, 11131分子

#2: 化合物...
ChemComp-SF4 / IRON/SULFUR CLUSTER / 鉄・硫黄クラスター


分子量: 351.640 Da / 分子数: 97 / 由来タイプ: 合成 / 式: Fe4S4 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD / フラビンアデニンジヌクレオチド


分子量: 785.550 Da / 分子数: 17 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#4: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル / エチレングリコール


分子量: 62.068 Da / 分子数: 123 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物
ChemComp-SRM / SIROHEME / シロヘム


分子量: 916.661 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C42H44FeN4O16 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 31 / 由来タイプ: 合成 / 式: SO4
#7: 化合物
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / 硫化水素 / 硫化水素


分子量: 34.081 Da / 分子数: 16 / 由来タイプ: 合成 / 式: H2S / タイプ: SUBJECT OF INVESTIGATION
#8: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド / 塩化物


分子量: 35.453 Da / 分子数: 29 / 由来タイプ: 合成 / 式: Cl
#9: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 19 / 由来タイプ: 合成 / 式: C3H8O3
#10: 化合物
ChemComp-LI / LITHIUM ION / リチウムカチオン / リチウム


分子量: 6.941 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Li
#11: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル / ジエチレングリコール


分子量: 106.120 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C4H10O3
#12: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム / トリスヒドロキシメチルアミノメタン


分子量: 122.143 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#13: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 10772 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.98 Å3/Da / 溶媒含有率: 58.68 % / 解説: Thick square-shaped brown crystals
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM ...詳細: Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, 0.5 mM FAD and 0.0155 mM F420H2. 0.6 ul of sample was mixed with 0.6 ul reservoir solution. The reservoir solution contained 0.2 M Lithium sulfate, 0.1 M Bis-Tris, pH 5.5 and 25 % w/v Polyethylene glycol 3350. Crystals appeared after few days.
PH範囲: / / Temp details: +/- 1 degree of oscillation

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1.00004 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2020年3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: 1.00004 Å / 相対比: 1
反射解像度: 1.55→121.276 Å / Num. obs: 1396397 / % possible obs: 94.5 % / 冗長度: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.075 / Rrim(I) all: 0.198 / Net I/σ(I): 8.7
反射 シェル解像度: 1.55→1.689 Å / 冗長度: 6.9 % / Rmerge(I) obs: 1.623 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 69018 / CC1/2: 0.439 / Rpim(I) all: 0.664 / Rrim(I) all: 1.755 / % possible all: 70.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.27データ抽出
autoPROCデータ削減
autoPROCデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7NP8

7np8


解像度: 1.55→77.29 Å / SU ML: 0.13 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 18.34 / 立体化学のターゲット値: ML
詳細: The last refinement cycles were performed with hydrogens in riding position.
Rfactor反射数%反射
Rfree0.1711 69210 4.96 %
Rwork0.1588 1326976 -
obs0.1594 1396186 75.51 %
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: 141.69 Å2 / Biso mean: 26.3738 Å2 / Biso min: 5.3 Å2
精密化ステップサイクル: final / 解像度: 1.55→77.29 Å
タンパク質核酸リガンド溶媒全体
原子数77290 0 3554 10774 91618
Biso mean--23.43 35.95 -
残基数----9879
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A26768X-RAY DIFFRACTION7.14TORSIONAL
12B26768X-RAY DIFFRACTION7.14TORSIONAL
13C26768X-RAY DIFFRACTION7.14TORSIONAL
14D26768X-RAY DIFFRACTION7.14TORSIONAL
15E26768X-RAY DIFFRACTION7.14TORSIONAL
16F26768X-RAY DIFFRACTION7.14TORSIONAL
17G26768X-RAY DIFFRACTION7.14TORSIONAL
18H26768X-RAY DIFFRACTION7.14TORSIONAL
19I26768X-RAY DIFFRACTION7.14TORSIONAL
110J26768X-RAY DIFFRACTION7.14TORSIONAL
111K26768X-RAY DIFFRACTION7.14TORSIONAL
112L26768X-RAY DIFFRACTION7.14TORSIONAL
113M26768X-RAY DIFFRACTION7.14TORSIONAL
114N26768X-RAY DIFFRACTION7.14TORSIONAL
115O26768X-RAY DIFFRACTION7.14TORSIONAL
116P26768X-RAY DIFFRACTION7.14TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.3369900.3033170417943
1.57-1.590.33221700.3014323234026
1.59-1.610.32623200.2835637595710
1.61-1.630.31354550.28838854930915
1.63-1.650.29866740.2847122801295421
1.65-1.670.29658600.2785169181777829
1.67-1.690.283811950.2703225712376639
1.69-1.720.28615600.2635286323019249
1.72-1.750.277119990.2549371993919864
1.75-1.780.271624020.2535457854818778
1.78-1.810.256426350.2459511645379987
1.81-1.840.244827490.2318536795642892
1.84-1.870.238127880.2198555885837695
1.87-1.910.228529640.214571866015098
1.91-1.950.210630210.1965573126033398
1.95-20.212228700.1847575956046598
2-2.050.190228780.1738576466052498
2.05-2.10.183730180.1642576236064198
2.1-2.170.166929990.153576266062598
2.17-2.240.171331110.1489575806069199
2.24-2.320.157830680.1399577306079899
2.32-2.410.15930850.1426579266101199
2.41-2.520.152730980.1392577916088999
2.52-2.650.153129570.1402580726102999
2.65-2.820.161630080.1451581946120299
2.82-3.040.155329830.1458582166119999
3.04-3.340.152430770.1424582066128399
3.34-3.820.137730850.13045824761332100
3.82-4.820.120130080.11355850861516100
4.82-77.290.151230830.15015827561358100
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99440.4419-0.17130.7812-0.110.6630.0581-0.171-0.07550.0922-0.08330.00080.0452-0.0280.01960.087-0.02030.00250.12110.00490.093366.98350.579-64.669
20.18150.044-0.23730.1319-0.06850.8624-0.00670.0293-0.0017-0.0115-0.00770.02370.0397-0.06350.02560.0694-0.001-0.01110.06910.00850.090678.64959.802-104.886
31.3779-0.5651-0.29550.7951-0.36270.96760.0370.2039-0.0648-0.1012-0.03380.08790.05-0.09620.00650.1113-0.0048-0.0310.12560.04660.106277.73976.669-141.999
42.7374-0.54360.20841.80880.12440.8981-0.00670.12940.34850.0530.0598-0.0371-0.3895-0.0275-0.01130.28770.0422-0.03140.11120.06260.225376.108106.543-141.474
52.37110.05110.68131.0235-0.40771.14650.03550.25850.1645-0.0737-0.1177-0.0736-0.22670.040.06390.20490.0336-0.01220.19870.09120.17881.14495.161-152.215
60.7605-0.46740.43411.1105-0.56371.10130.02550.12190.0649-0.048-0.00140.1237-0.138-0.1809-0.00970.16080.0396-0.02480.19610.04970.139370.24491.382-146.667
71.99120.70380.13573.44230.14721.04860.0481-0.02670.20270.1635-0.03340.3258-0.265-0.2577-0.00910.21080.08160.00380.19960.04290.111664.24395.173-135.94
80.353-0.01850.27020.1675-0.13821.0573-0.00150.02490.0323-0.01120.01480.0551-0.0971-0.1290.00390.08530.0193-0.00030.08020.0120.111674.71577.766-104.272
90.12380.06360.3770.0843-0.14533.9723-0.00070.01290.06080.03140.00050.016-0.1961-0.08620.01140.08760.00360.00070.07450.01290.117889.55878.685-90.171
101.3629-0.1545-0.47950.84360.32372.71850.0177-0.01310.1854-0.00670.0043-0.0373-0.28490.1308-0.03290.1177-0.0139-0.01280.07560.03740.122692.97688.085-111.177
111.11580.59790.0631.08240.24450.82640.086-0.15660.1170.1396-0.10110.0468-0.1077-0.00490.01440.141-0.0508-0.0090.1380.0040.1168123.57286.321-63.191
120.78680.29640.07490.71620.17440.55080.0463-0.13820.06240.0923-0.044-0.0944-0.06840.1048-0.00030.1785-0.0681-0.02270.16920.02580.1279134.17187.708-65.16
130.20360.05860.15070.21140.05470.75240.00380.03820.0326-0.0014-0.0143-0.034-0.07720.10610.01980.0832-0.01720.00390.08990.0250.1008119.55875.864-104.217
140.9227-0.2275-0.20221.1137-0.01150.8972-0.00390.2112-0.1952-0.3218-0.0627-0.14970.20730.10130.02980.24240.04960.06370.1989-0.02610.1768124.9543.107-143.521
150.2649-0.0058-0.2070.18660.03780.633-0.00660.0009-0.0495-0.0291-0.0188-0.05250.07060.10440.02650.08410.0181-0.00090.09990.02230.1165119.98253.084-106.996
161.4901-0.4450.31130.827-0.16690.91-0.0605-0.2056-0.08880.27740.099-0.19730.25670.2231-0.00770.27810.0808-0.06410.19220.01880.208863.437-20.237-59.261
170.1719-0.02750.04810.423-0.01030.82620.00980.0088-0.0538-0.0164-0.0111-0.08780.16620.14530.01390.10340.02910.02180.109-0.00510.158155.507-16.038-96.624
180.68750.43040.31611.14250.19340.88720.0080.1468-0.0378-0.4378-0.04180.2962-0.0328-0.1280.04250.38170.0308-0.09470.2185-0.090.258424.357-17.877-139.755
190.3665-0.09710.19890.54890.2690.84490.06850.1339-0.1665-0.1852-0.10430.18530.1863-0.1491-0.0110.324-0.0206-0.02730.2122-0.10320.302226.78-33.358-130.902
200.17030.02690.1220.29230.20590.8838-0.0031-0.0008-0.0661-0.006-0.03780.05510.097-0.11470.06050.0778-0.02520.01490.0844-0.01350.1430.759-9.078-96.597
211.3511-0.5694-0.24780.98420.06550.863-0.0899-0.1691-0.0430.12670.0370.12830.036-0.06430.04490.0939-0.00520.01380.0973-0.01720.101822.18828.268-63.248
220.7122-0.2146-0.28740.30180.37361.8592-0.0891-0.35660.31180.25460.0555-0.0225-0.2839-0.06390.01710.28560.0567-0.02930.2652-0.11020.276116.31446.369-54.831
230.1668-0.0659-0.14170.29690.21950.64310.00360.00590.0588-0.0523-0.03260.0492-0.1317-0.04230.01790.09130.0014-0.02160.07720.00280.112229.81636.685-90.437
240.2986-0.0263-0.25440.27810.16221.4816-0.01430.0558-0.0135-0.0755-0.030.05650.0454-0.14680.06950.0974-0.0146-0.01710.0737-0.00760.108729.55913.662-109.812
250.96640.5345-0.26950.8689-0.10110.8233-0.05670.1776-0.0462-0.25450.0819-0.1517-0.05580.0895-0.02350.2679-0.0270.0670.17650.00630.14562.08128.434-140.27
260.03370.0308-0.13680.0342-0.1520.753-0.04180.30430.2656-0.35170.12050.0448-0.32380.0727-0.08560.5438-0.11620.06160.35960.10770.281866.52147.09-148.802
271.7457-0.1266-0.05110.60990.04070.6850.0471-0.01380.2367-0.03760.0218-0.1076-0.25250.11760.00310.318-0.06390.08550.21580.02460.192366.19344.348-132.124
280.19-0.0386-0.0790.248-0.06710.717-0.00180.03650.0242-0.0495-0.0185-0.0654-0.09510.06640.02370.0851-0.02810.00970.08630.01030.112552.27825.71-100.802
291.03380.4922-0.07480.6648-0.14470.40570.0826-0.1945-0.06770.1076-0.1088-0.01310.0518-0.02570.02740.1673-0.08580.01550.2185-0.02680.126559.82321.5152.52
300.13070.0173-0.20820.2408-0.06020.74430.00210.0430.00850.0003-0.0570.03940.1022-0.19570.05580.0971-0.03570.00980.1851-0.03370.10569.33532.49512.489
310.9421-0.40090.28740.9575-0.22190.70550.01830.11250.2003-0.1916-0.1344-0.0279-0.2029-0.16070.09740.22660.1125-0.0280.26130.01520.164468.05362.976-24.848
320.1711-0.02690.26930.4784-0.06760.5341-0.0579-0.01780.1875-0.2299-0.12030.2831-0.2865-0.4230.08420.35050.2194-0.12450.5116-0.08260.354451.21469.882-25.476
330.1936-0.04470.03310.1641-0.00140.56960.00020.03930.0255-0.0316-0.05150.0277-0.038-0.22950.04820.07940.01820.00310.1973-0.02210.125171.36952.66614.318
341.04790.59630.05961.14380.33220.73770.0363-0.1030.040.0466-0.0767-0.0533-0.0255-0.03240.0460.05520.0093-0.02040.09710.01950.1323116.61654.22849.515
355.023-0.56431.86531.0281-0.03131.51030.0161-0.33790.17320.1084-0.09060.1633-0.1113-0.23830.05760.10740.00280.00730.1417-0.02750.1766115.2763.81960.02
361.14020.44810.35220.78390.3210.8729-0.0082-0.08640.0420.03590.0056-0.0829-0.03140.05860.00440.0870.0057-0.01050.08980.02370.15124.92258.14353.673
371.2557-0.0422-0.08053.2510.05450.77210.0290.03610.1121-0.1486-0.0577-0.3084-0.09040.09190.03290.1128-0.0355-0.02150.12360.02990.1231130.5860.40742.66
380.25890.05110.39140.1780.00480.9560.0210.0634-0.0088-0.0054-0.0093-0.09450.01110.1396-0.00170.07120.02160.01820.11390.02160.152119.08545.36417.277
390.06410.06950.38550.40110.51262.2174-0.01830.02820.0184-0.1128-0.0101-0.0356-0.15750.00150.0370.08840.02840.0240.12530.02480.13499.52751.334-1.393
403.4833-0.51840.80693.9043-1.50723.3956-0.00770.0220.16330.02250.0390.1411-0.2365-0.2025-0.06010.06350.02680.01390.0857-0.02520.102297.32257.88622.299
410.757-0.4666-0.11711.1410.34621.06970.06150.1427-0.069-0.1594-0.07390.0220.1096-0.01420.00860.16770.04380.04930.17950.00420.1356109.70419.208-28.794
420.4508-0.169-0.31510.75970.26431.25560.01920.05620.0024-0.1146-0.0105-0.12890.15290.2044-0.02070.1930.06550.05330.1830.01740.1546117.95716.767-30.256
431.81360.7865-0.17562.9178-0.14181.11770.0578-0.1044-0.08740.0545-0.0076-0.28360.21610.2881-0.03980.23060.10.03710.2326-0.00610.1309124.01613.223-19.53
440.20160.0048-0.08350.18150.12320.82630.01030.0229-0.0303-0.0137-0.0145-0.06830.12090.05810.01150.0950.02620.01040.07990.0140.1224108.12928.55512.614
451.1332-0.3423-0.10361.87280.23591.0098-0.087-0.1398-0.10830.2425-0.02290.00140.0529-0.01490.11250.1109-0.00160.0120.07990.04740.16242.458-44.82852.051
461.0683-0.18240.11111.48340.2321.2448-0.01450.0075-0.01680.0319-0.0794-0.26050.03470.31670.06790.12590.01510.01930.2870.18850.47471.988-48.78949.235
470.89770.32970.05824.1428-1.47731.0775-0.0598-0.1811-0.00880.3121-0.1085-0.3046-0.17470.23160.12170.1947-0.0326-0.07110.22160.10590.334361.752-43.74561.087
481.0521-0.76950.34440.802-0.36230.722-0.0584-0.02290.00850.1124-0.0828-0.1888-0.04020.09250.13220.1342-0.00520.00250.10830.06270.224452.507-41.21248.397
490.139-0.0415-0.12070.0289-0.06880.997-0.0698-0.1551-0.19690.0911-0.1502-0.20890.3360.17480.05860.28880.03990.02450.22840.15810.412359.908-63.20959.794
502.57470.4054-0.39770.35960.0560.472-0.09420.1193-0.3527-0.0677-0.0862-0.23790.19880.12650.14020.18340.05010.06570.19320.10380.383759.16-59.34943.861
510.1876-0.0761-0.0130.2835-0.10040.5794-0.06920.044-0.1618-0.0375-0.0621-0.00170.247-0.05760.11440.1617-0.02520.05360.1019-0.03640.206441.573-49.4819.414
520.4558-0.19510.40910.4933-0.01982.7127-0.00460.094-0.0343-0.1008-0.0691-0.0013-0.06130.07570.07380.0871-0.00990.00350.0763-0.01920.125146.172-28.6666.587
530.28120.20580.18140.23240.03060.16710.05020.1191-0.0233-0.205-0.03650.28130.0778-0.09450.090.33290.068-0.25410.3652-0.37960.31849.348-42.902-24.276
540.3523-0.17620.05690.2293-0.24210.31430.1115-0.03850.0047-0.1752-0.00130.120.2561-0.0315-0.12630.3536-0.0414-0.08360.3799-0.2230.46978.147-59.589-24.787
550.1919-0.0854-0.05410.25040.14280.652-0.0620.1086-0.1385-0.0283-0.11390.11450.1165-0.21670.10830.1242-0.05550.02510.1847-0.11070.249323.566-40.84515.109
561.4078-0.2329-0.16571.81110.05791.2321-0.0288-0.1552-0.01550.35570.00160.008-0.06510.08290.04240.1358-0.00960.01470.0654-0.01330.090626.3980.58853.926
571.2932-0.46280.18372.05490.12951.4397-0.0221-0.0846-0.18120.20610.02180.4244-0.0182-0.39890.07260.13820.03820.06850.2271-0.02720.3339-3.115.12253.452
581.00940.04190.24963.04190.89191.6957-0.0945-0.1969-0.15290.43770.06550.21850.1019-0.22490.02150.27460.01520.11690.16670.02730.23477.743-1.06464.075
591.2681-0.5056-0.32920.88650.3670.9965-0.0601-0.16250.11460.26190.04520.0854-0.1648-0.06990.01720.22850.02120.03080.1173-0.02180.161312.579.51358.632
604.20360.30770.26831.29170.04480.7818-0.01140.05690.30770.0042-0.01910.2653-0.193-0.12610.04130.19160.04310.03170.1276-0.01080.12429.38315.88748.008
610.31650.0945-0.06160.47750.19021.280.07780.0670.063-0.0873-0.08050.0863-0.2424-0.09680.01950.16220.0528-0.02280.1075-0.00940.143826.07411.53524.678
620.1346-0.0455-0.09010.23670.1161.11860.06780.1718-0.0709-0.185-0.12640.1704-0.0632-0.21780.04180.17560.0735-0.09380.2206-0.06740.160821.482-9.7494.923
631.45320.1120.37431.27710.12151.29260.01680.0935-0.1899-0.0644-0.07750.25110.0935-0.29-0.03030.0887-0.0077-0.01630.1811-0.06870.201215.239-15.94925.356
640.61340.1694-0.02190.60090.0550.60340.04810.3470.0458-0.67690.1258-0.2052-0.51360.10450.04580.8262-0.01730.14510.31090.0170.113152.088.424-25.423
650.31510.0391-0.23720.56760.14910.8240.05070.07080.0326-0.1855-0.0208-0.0508-0.2340.0323-0.01050.15470.0056-0.00450.09530.00640.102844.9791.8411.572
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:330 )A1 - 330
2X-RAY DIFFRACTION2( CHAIN A AND RESID 331:618 )A331 - 618
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:69 )B1 - 69
4X-RAY DIFFRACTION4( CHAIN B AND RESID 70:100 )B70 - 100
5X-RAY DIFFRACTION5( CHAIN B AND RESID 101:150 )B101 - 150
6X-RAY DIFFRACTION6( CHAIN B AND RESID 151:280 )B151 - 280
7X-RAY DIFFRACTION7( CHAIN B AND RESID 281:330 )B281 - 330
8X-RAY DIFFRACTION8( CHAIN B AND RESID 331:520 )B331 - 520
9X-RAY DIFFRACTION9( CHAIN B AND RESID 521:563 )B521 - 563
10X-RAY DIFFRACTION10( CHAIN B AND RESID 564:618 )B564 - 618
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1:150 )C1 - 150
12X-RAY DIFFRACTION12( CHAIN C AND RESID 151:330 )C151 - 330
13X-RAY DIFFRACTION13( CHAIN C AND RESID 331:618 )C331 - 618
14X-RAY DIFFRACTION14( CHAIN D AND RESID 2:280 )D2 - 280
15X-RAY DIFFRACTION15( CHAIN D AND RESID 281:618 )D281 - 618
16X-RAY DIFFRACTION16( CHAIN E AND RESID 2:280 )E2 - 280
17X-RAY DIFFRACTION17( CHAIN E AND RESID 281:618 )E281 - 618
18X-RAY DIFFRACTION18( CHAIN F AND RESID 1:205 )F1 - 205
19X-RAY DIFFRACTION19( CHAIN F AND RESID 206:396 )F206 - 396
20X-RAY DIFFRACTION20( CHAIN F AND RESID 397:618 )F397 - 618
21X-RAY DIFFRACTION21( CHAIN G AND RESID 1:205 )G1 - 205
22X-RAY DIFFRACTION22( CHAIN G AND RESID 206:280 )G206 - 280
23X-RAY DIFFRACTION23( CHAIN G AND RESID 281:491 )G281 - 491
24X-RAY DIFFRACTION24( CHAIN G AND RESID 492:618 )G492 - 618
25X-RAY DIFFRACTION25( CHAIN H AND RESID 2:205 )H2 - 205
26X-RAY DIFFRACTION26( CHAIN H AND RESID 206:280 )H206 - 280
27X-RAY DIFFRACTION27( CHAIN H AND RESID 281:330 )H281 - 330
28X-RAY DIFFRACTION28( CHAIN H AND RESID 331:618 )H331 - 618
29X-RAY DIFFRACTION29( CHAIN I AND RESID 1:330 )I1 - 330
30X-RAY DIFFRACTION30( CHAIN I AND RESID 331:618 )I331 - 618
31X-RAY DIFFRACTION31( CHAIN J AND RESID 1:205 )J1 - 205
32X-RAY DIFFRACTION32( CHAIN J AND RESID 206:330 )J206 - 330
33X-RAY DIFFRACTION33( CHAIN J AND RESID 331:618 )J331 - 618
34X-RAY DIFFRACTION34( CHAIN K AND RESID 2:100 )K2 - 100
35X-RAY DIFFRACTION35( CHAIN K AND RESID 101:150 )K101 - 150
36X-RAY DIFFRACTION36( CHAIN K AND RESID 151:280 )K151 - 280
37X-RAY DIFFRACTION37( CHAIN K AND RESID 281:330 )K281 - 330
38X-RAY DIFFRACTION38( CHAIN K AND RESID 331:491 )K331 - 491
39X-RAY DIFFRACTION39( CHAIN K AND RESID 492:587 )K492 - 587
40X-RAY DIFFRACTION40( CHAIN K AND RESID 588:618 )K588 - 618
41X-RAY DIFFRACTION41( CHAIN L AND RESID 2:150 )L2 - 150
42X-RAY DIFFRACTION42( CHAIN L AND RESID 151:280 )L151 - 280
43X-RAY DIFFRACTION43( CHAIN L AND RESID 281:330 )L281 - 330
44X-RAY DIFFRACTION44( CHAIN L AND RESID 331:618 )L331 - 618
45X-RAY DIFFRACTION45( CHAIN M AND RESID 2:69 )M2 - 69
46X-RAY DIFFRACTION46( CHAIN M AND RESID 70:100 )M70 - 100
47X-RAY DIFFRACTION47( CHAIN M AND RESID 101:150 )M101 - 150
48X-RAY DIFFRACTION48( CHAIN M AND RESID 151:205 )M151 - 205
49X-RAY DIFFRACTION49( CHAIN M AND RESID 206:280 )M206 - 280
50X-RAY DIFFRACTION50( CHAIN M AND RESID 281:330 )M281 - 330
51X-RAY DIFFRACTION51( CHAIN M AND RESID 331:491 )M331 - 491
52X-RAY DIFFRACTION52( CHAIN M AND RESID 492:618 )M492 - 618
53X-RAY DIFFRACTION53( CHAIN N AND RESID 2:205 )N2 - 205
54X-RAY DIFFRACTION54( CHAIN N AND RESID 206:330 )N206 - 330
55X-RAY DIFFRACTION55( CHAIN N AND RESID 331:618 )N331 - 618
56X-RAY DIFFRACTION56( CHAIN O AND RESID 2:69 )O2 - 69
57X-RAY DIFFRACTION57( CHAIN O AND RESID 70:100 )O70 - 100
58X-RAY DIFFRACTION58( CHAIN O AND RESID 101:150 )O101 - 150
59X-RAY DIFFRACTION59( CHAIN O AND RESID 151:280 )O151 - 280
60X-RAY DIFFRACTION60( CHAIN O AND RESID 281:330 )O281 - 330
61X-RAY DIFFRACTION61( CHAIN O AND RESID 331:452 )O331 - 452
62X-RAY DIFFRACTION62( CHAIN O AND RESID 453:587 )O453 - 587
63X-RAY DIFFRACTION63( CHAIN O AND RESID 588:618 )O588 - 618
64X-RAY DIFFRACTION64( CHAIN P AND RESID 2:280 )P2 - 280
65X-RAY DIFFRACTION65( CHAIN P AND RESID 281:618 )P281 - 618

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万見について

-
お知らせ

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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

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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

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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

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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

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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

他の情報も見る