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- PDB-6zgp: Crystal structure of the quaternary ammonium Rieske monooxygenase... -

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基本情報

登録情報
データベース: PDB / ID: 6zgp
タイトルCrystal structure of the quaternary ammonium Rieske monooxygenase CntA in complex with inhibitor MMV12 (MMV020670)
要素Carnitine monooxygenase oxygenase subunit
キーワードOXIDOREDUCTASE / Apo / Rieske / Iron-Sulphur Cluster
機能・相同性
機能・相同性情報


carnitine monooxygenase / carnitine metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
類似検索 - 分子機能
Carnitine monooxygenase oxygenase subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
類似検索 - ドメイン・相同性
: / FE2/S2 (INORGANIC) CLUSTER / Chem-QKQ / Carnitine monooxygenase oxygenase subunit
類似検索 - 構成要素
生物種Acinetobacter baumannii (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: 2.01 Å
データ登録者Quareshy, M. / Shanmugam, M. / Bugg, T.D.H. / Cameron, A. / Chen, Y.
資金援助 英国, 1件
組織認可番号国
Leverhulme TrustRPG-2016-307 英国
引用ジャーナル: J.Biol.Chem. / 年: 2020
タイトル: Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer.
著者: Quareshy, M. / Shanmugam, M. / Townsend, E. / Jameson, E. / Bugg, T.D.H. / Cameron, A.D. / Chen, Y.
履歴
登録2020年6月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年11月18日Provider: repository / タイプ: Initial release
改定 1.12021年7月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
改定 1.22024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Carnitine monooxygenase oxygenase subunit
B: Carnitine monooxygenase oxygenase subunit
C: Carnitine monooxygenase oxygenase subunit
D: Carnitine monooxygenase oxygenase subunit
E: Carnitine monooxygenase oxygenase subunit
F: Carnitine monooxygenase oxygenase subunit
G: Carnitine monooxygenase oxygenase subunit
H: Carnitine monooxygenase oxygenase subunit
I: Carnitine monooxygenase oxygenase subunit
J: Carnitine monooxygenase oxygenase subunit
K: Carnitine monooxygenase oxygenase subunit
L: Carnitine monooxygenase oxygenase subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)547,65160
ポリマ－537,36212
非ポリマー10,28948
水21,7621208
1
A: Carnitine monooxygenase oxygenase subunit
B: Carnitine monooxygenase oxygenase subunit
C: Carnitine monooxygenase oxygenase subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,91315
ポリマ－134,3413
非ポリマー2,57212
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-67 kcal/mol
Surface area40230 Å2
手法PISA
2
D: Carnitine monooxygenase oxygenase subunit
E: Carnitine monooxygenase oxygenase subunit
F: Carnitine monooxygenase oxygenase subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,91315
ポリマ－134,3413
非ポリマー2,57212
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-65 kcal/mol
Surface area41120 Å2
手法PISA
3
G: Carnitine monooxygenase oxygenase subunit
H: Carnitine monooxygenase oxygenase subunit
I: Carnitine monooxygenase oxygenase subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,91315
ポリマ－134,3413
非ポリマー2,57212
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-65 kcal/mol
Surface area40820 Å2
手法PISA
4
J: Carnitine monooxygenase oxygenase subunit
K: Carnitine monooxygenase oxygenase subunit
L: Carnitine monooxygenase oxygenase subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,91315
ポリマ－134,3413
非ポリマー2,57212
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-66 kcal/mol
Surface area40350 Å2
手法PISA
単位格子
Length a, b, c (Å)91.070, 173.770, 157.290
Angle α, β, γ (deg.)90.000, 90.150, 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 A and (resid 3 through 4 or resid 6...
21(chain B and (resid 3 through 4 or resid 6...
31(chain C and (resid 3 through 4 or resid 6...
41(chain D and (resid 3 through 4 or resid 6...
51(chain E and (resid 3 through 4 or resid 6...
61(chain F and (resid 3 through 4 or resid 6...
71(chain G and (resid 3 through 4 or resid 6...
81(chain H and (resid 3 through 4 or resid 6...
91(chain I and (resid 3 through 4 or resid 6...
101(chain J and (resid 3 through 4 or resid 6...
111(chain K and (resid 3 through 4 or resid 6...
121(chain L and (resid 3 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 3 through 4 or resid 6...A3 - 4
121(chain A and (resid 3 through 4 or resid 6...A6 - 29
131(chain A and (resid 3 through 4 or resid 6...A0
141(chain A and (resid 3 through 4 or resid 6...A7
151(chain A and (resid 3 through 4 or resid 6...A10113
161(chain A and (resid 3 through 4 or resid 6...A115 - 12
171(chain A and (resid 3 through 4 or resid 6...A124 - 132
181(chain A and (resid 3 through 4 or resid 6...A135 - 155
191(chain A and (resid 3 through 4 or resid 6...A157 - 169
1101(chain A and (resid 3 through 4 or resid 6...A171 - 179
1111(chain A and (resid 3 through 4 or resid 6...A181 - 21240
1121(chain A and (resid 3 through 4 or resid 6...A25630
1131(chain A and (resid 3 through 4 or resid 6...A232 - 240
1141(chain A and (resid 3 through 4 or resid 6...A256 - 302
1151(chain A and (resid 3 through 4 or resid 6...A350 - 481
1161(chain A and (resid 3 through 4 or resid 6...A501
1171(chain A and (resid 3 through 4 or resid 6...A601
211(chain B and (resid 3 through 4 or resid 6...B3 - 4
221(chain B and (resid 3 through 4 or resid 6...B6 - 29
231(chain B and (resid 3 through 4 or resid 6...B31 - 62
241(chain B and (resid 3 through 4 or resid 6...B108
251(chain B and (resid 3 through 4 or resid 6...B3 - 371
261(chain B and (resid 3 through 4 or resid 6...B2 - 113
271(chain B and (resid 3 through 4 or resid 6...B115 - 122
281(chain B and (resid 3 through 4 or resid 6...B135 - 155
291(chain B and (resid 3 through 4 or resid 6...B181 - 219
2101(chain B and (resid 3 through 4 or resid 6...B181 - 218
2111(chain B and (resid 3 through 4 or resid 6...B220 - 230
2121(chain B and (resid 3 through 4 or resid 6...B256 - 302
2131(chain B and (resid 3 through 4 or resid 6...B304 - 348
2141(chain B and (resid 3 through 4 or resid 6...B350 - 488
2151(chain B and (resid 3 through 4 or resid 6...B350 - 481
2161(chain B and (resid 3 through 4 or resid 6...B501
2171(chain B and (resid 3 through 4 or resid 6...B601
311(chain C and (resid 3 through 4 or resid 6...C3 - 4
321(chain C and (resid 3 through 4 or resid 6...C6 - 29
331(chain C and (resid 3 through 4 or resid 6...C31 - 62
341(chain C and (resid 3 through 4 or resid 6...C108
351(chain C and (resid 3 through 4 or resid 6...C3 - 371
361(chain C and (resid 3 through 4 or resid 6...C2 - 113
371(chain C and (resid 3 through 4 or resid 6...C115 - 122
381(chain C and (resid 3 through 4 or resid 6...C135 - 155
391(chain C and (resid 3 through 4 or resid 6...C181 - 219
3101(chain C and (resid 3 through 4 or resid 6...C181 - 218
3111(chain C and (resid 3 through 4 or resid 6...C220 - 230
3121(chain C and (resid 3 through 4 or resid 6...C256 - 302
3131(chain C and (resid 3 through 4 or resid 6...C304 - 348
3141(chain C and (resid 3 through 4 or resid 6...C350 - 488
3151(chain C and (resid 3 through 4 or resid 6...C350 - 481
3161(chain C and (resid 3 through 4 or resid 6...C501
3171(chain C and (resid 3 through 4 or resid 6...C601
411(chain D and (resid 3 through 4 or resid 6...D3 - 4
421(chain D and (resid 3 through 4 or resid 6...D6 - 29
431(chain D and (resid 3 through 4 or resid 6...D31 - 62
441(chain D and (resid 3 through 4 or resid 6...D108
451(chain D and (resid 3 through 4 or resid 6...D3 - 371
461(chain D and (resid 3 through 4 or resid 6...D2 - 113
471(chain D and (resid 3 through 4 or resid 6...D115 - 122
481(chain D and (resid 3 through 4 or resid 6...D135 - 155
491(chain D and (resid 3 through 4 or resid 6...D181 - 219
4101(chain D and (resid 3 through 4 or resid 6...D181 - 218
4111(chain D and (resid 3 through 4 or resid 6...D220 - 230
4121(chain D and (resid 3 through 4 or resid 6...D256 - 302
4131(chain D and (resid 3 through 4 or resid 6...D304 - 348
4141(chain D and (resid 3 through 4 or resid 6...D350 - 488
4151(chain D and (resid 3 through 4 or resid 6...D350 - 481
4161(chain D and (resid 3 through 4 or resid 6...D501
4171(chain D and (resid 3 through 4 or resid 6...D601
511(chain E and (resid 3 through 4 or resid 6...E3 - 4
521(chain E and (resid 3 through 4 or resid 6...E6 - 29
531(chain E and (resid 3 through 4 or resid 6...E31 - 62
541(chain E and (resid 3 through 4 or resid 6...E108
551(chain E and (resid 3 through 4 or resid 6...E3 - 371
561(chain E and (resid 3 through 4 or resid 6...E2 - 113
571(chain E and (resid 3 through 4 or resid 6...E115 - 122
581(chain E and (resid 3 through 4 or resid 6...E135 - 155
591(chain E and (resid 3 through 4 or resid 6...E181 - 219
5101(chain E and (resid 3 through 4 or resid 6...E181 - 218
5111(chain E and (resid 3 through 4 or resid 6...E220 - 230
5121(chain E and (resid 3 through 4 or resid 6...E256 - 302
5131(chain E and (resid 3 through 4 or resid 6...E304 - 348
5141(chain E and (resid 3 through 4 or resid 6...E350 - 488
5151(chain E and (resid 3 through 4 or resid 6...E350 - 481
5161(chain E and (resid 3 through 4 or resid 6...E501
5171(chain E and (resid 3 through 4 or resid 6...E601
611(chain F and (resid 3 through 4 or resid 6...F3 - 4
621(chain F and (resid 3 through 4 or resid 6...F6 - 29
631(chain F and (resid 3 through 4 or resid 6...F31 - 62
641(chain F and (resid 3 through 4 or resid 6...F108
651(chain F and (resid 3 through 4 or resid 6...F3 - 371
661(chain F and (resid 3 through 4 or resid 6...F2 - 113
671(chain F and (resid 3 through 4 or resid 6...F115 - 122
681(chain F and (resid 3 through 4 or resid 6...F135 - 155
691(chain F and (resid 3 through 4 or resid 6...F181 - 219
6101(chain F and (resid 3 through 4 or resid 6...F181 - 218
6111(chain F and (resid 3 through 4 or resid 6...F220 - 230
6121(chain F and (resid 3 through 4 or resid 6...F256 - 302
6131(chain F and (resid 3 through 4 or resid 6...F304 - 348
6141(chain F and (resid 3 through 4 or resid 6...F350 - 488
6151(chain F and (resid 3 through 4 or resid 6...F350 - 481
6161(chain F and (resid 3 through 4 or resid 6...F501
6171(chain F and (resid 3 through 4 or resid 6...F601
711(chain G and (resid 3 through 4 or resid 6...G3 - 4
721(chain G and (resid 3 through 4 or resid 6...G6 - 29
731(chain G and (resid 3 through 4 or resid 6...G31 - 62
741(chain G and (resid 3 through 4 or resid 6...G108
751(chain G and (resid 3 through 4 or resid 6...G3 - 371
761(chain G and (resid 3 through 4 or resid 6...G2 - 113
771(chain G and (resid 3 through 4 or resid 6...G115 - 122
781(chain G and (resid 3 through 4 or resid 6...G135 - 155
791(chain G and (resid 3 through 4 or resid 6...G181 - 219
7101(chain G and (resid 3 through 4 or resid 6...G181 - 218
7111(chain G and (resid 3 through 4 or resid 6...G220 - 230
7121(chain G and (resid 3 through 4 or resid 6...G256 - 302
7131(chain G and (resid 3 through 4 or resid 6...G304 - 348
7141(chain G and (resid 3 through 4 or resid 6...G350 - 488
7151(chain G and (resid 3 through 4 or resid 6...G350 - 481
7161(chain G and (resid 3 through 4 or resid 6...G501
7171(chain G and (resid 3 through 4 or resid 6...G601
811(chain H and (resid 3 through 4 or resid 6...H3 - 4
821(chain H and (resid 3 through 4 or resid 6...H6 - 29
831(chain H and (resid 3 through 4 or resid 6...H31 - 62
841(chain H and (resid 3 through 4 or resid 6...H108
851(chain H and (resid 3 through 4 or resid 6...H3 - 371
861(chain H and (resid 3 through 4 or resid 6...H2 - 113
871(chain H and (resid 3 through 4 or resid 6...H115 - 122
881(chain H and (resid 3 through 4 or resid 6...H135 - 155
891(chain H and (resid 3 through 4 or resid 6...H181 - 219
8101(chain H and (resid 3 through 4 or resid 6...H181 - 218
8111(chain H and (resid 3 through 4 or resid 6...H220 - 230
8121(chain H and (resid 3 through 4 or resid 6...H256 - 302
8131(chain H and (resid 3 through 4 or resid 6...H304 - 348
8141(chain H and (resid 3 through 4 or resid 6...H350 - 488
8151(chain H and (resid 3 through 4 or resid 6...H350 - 481
8161(chain H and (resid 3 through 4 or resid 6...H501
8171(chain H and (resid 3 through 4 or resid 6...H601
911(chain I and (resid 3 through 4 or resid 6...I3 - 4
921(chain I and (resid 3 through 4 or resid 6...I6 - 29
931(chain I and (resid 3 through 4 or resid 6...I31 - 62
941(chain I and (resid 3 through 4 or resid 6...I108
951(chain I and (resid 3 through 4 or resid 6...I3 - 371
961(chain I and (resid 3 through 4 or resid 6...I2 - 113
971(chain I and (resid 3 through 4 or resid 6...I115 - 122
981(chain I and (resid 3 through 4 or resid 6...I135 - 155
991(chain I and (resid 3 through 4 or resid 6...I181 - 219
9101(chain I and (resid 3 through 4 or resid 6...I181 - 218
9111(chain I and (resid 3 through 4 or resid 6...I220 - 230
9121(chain I and (resid 3 through 4 or resid 6...I256 - 302
9131(chain I and (resid 3 through 4 or resid 6...I304 - 348
9141(chain I and (resid 3 through 4 or resid 6...I350 - 488
9151(chain I and (resid 3 through 4 or resid 6...I350 - 481
9161(chain I and (resid 3 through 4 or resid 6...I501
9171(chain I and (resid 3 through 4 or resid 6...I601
1011(chain J and (resid 3 through 4 or resid 6...J3 - 4
1021(chain J and (resid 3 through 4 or resid 6...J6 - 29
1031(chain J and (resid 3 through 4 or resid 6...J31 - 62
1041(chain J and (resid 3 through 4 or resid 6...J108
1051(chain J and (resid 3 through 4 or resid 6...J3 - 371
1061(chain J and (resid 3 through 4 or resid 6...J2 - 113
1071(chain J and (resid 3 through 4 or resid 6...J115 - 122
1081(chain J and (resid 3 through 4 or resid 6...J135 - 155
1091(chain J and (resid 3 through 4 or resid 6...J181 - 219
10101(chain J and (resid 3 through 4 or resid 6...J181 - 218
10111(chain J and (resid 3 through 4 or resid 6...J220 - 230
10121(chain J and (resid 3 through 4 or resid 6...J256 - 302
10131(chain J and (resid 3 through 4 or resid 6...J304 - 348
10141(chain J and (resid 3 through 4 or resid 6...J350 - 488
10151(chain J and (resid 3 through 4 or resid 6...J350 - 481
10161(chain J and (resid 3 through 4 or resid 6...J501
10171(chain J and (resid 3 through 4 or resid 6...J601
1111(chain K and (resid 3 through 4 or resid 6...K3 - 4
1121(chain K and (resid 3 through 4 or resid 6...K6 - 29
1131(chain K and (resid 3 through 4 or resid 6...K31 - 62
1141(chain K and (resid 3 through 4 or resid 6...K108
1151(chain K and (resid 3 through 4 or resid 6...K3 - 371
1161(chain K and (resid 3 through 4 or resid 6...K2 - 113
1171(chain K and (resid 3 through 4 or resid 6...K115 - 122
1181(chain K and (resid 3 through 4 or resid 6...K135 - 155
1191(chain K and (resid 3 through 4 or resid 6...K181 - 219
11101(chain K and (resid 3 through 4 or resid 6...K181 - 218
11111(chain K and (resid 3 through 4 or resid 6...K220 - 230
11121(chain K and (resid 3 through 4 or resid 6...K256 - 302
11131(chain K and (resid 3 through 4 or resid 6...K304 - 348
11141(chain K and (resid 3 through 4 or resid 6...K350 - 488
11151(chain K and (resid 3 through 4 or resid 6...K350 - 481
11161(chain K and (resid 3 through 4 or resid 6...K501
11171(chain K and (resid 3 through 4 or resid 6...K601
1211(chain L and (resid 3 through 4 or resid 6...L3 - 4
1221(chain L and (resid 3 through 4 or resid 6...L6 - 29
1231(chain L and (resid 3 through 4 or resid 6...L31 - 62
1241(chain L and (resid 3 through 4 or resid 6...L108
1251(chain L and (resid 3 through 4 or resid 6...L3 - 371
1261(chain L and (resid 3 through 4 or resid 6...L2 - 113
1271(chain L and (resid 3 through 4 or resid 6...L115 - 122
1281(chain L and (resid 3 through 4 or resid 6...L135 - 155
1291(chain L and (resid 3 through 4 or resid 6...L181 - 219
12101(chain L and (resid 3 through 4 or resid 6...L181 - 218
12111(chain L and (resid 3 through 4 or resid 6...L220 - 230
12121(chain L and (resid 3 through 4 or resid 6...L256 - 302
12131(chain L and (resid 3 through 4 or resid 6...L304 - 348
12141(chain L and (resid 3 through 4 or resid 6...L350 - 488
12151(chain L and (resid 3 through 4 or resid 6...L350 - 481
12161(chain L and (resid 3 through 4 or resid 6...L501
12171(chain L and (resid 3 through 4 or resid 6...L601

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要素

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タンパク質 , 1種, 12分子 ABCDEFGHIJKL

#1: タンパク質
Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit


分子量: 44780.172 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Acinetobacter baumannii (バクテリア)
遺伝子: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_ ...遺伝子: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, DOL94_04925, DVA79_16365, E2533_13315, E2536_16135, E5294_15630, E5979_13670, EA685_07170, EA686_01565, EA706_03020, EA722_03860, EA746_003300, EWO92_12480, EWO96_16565, EWP49_15025, FD887_09300, FD913_14110, FJU36_15000, FJU42_16200, FJU76_14830, FJU79_08840, FJU87_10695, FJV14_20515, LV38_02893, NCTC13305_01609, SAMEA104305283_02985, SAMEA104305351_01970
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A059ZPP5, carnitine monooxygenase

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非ポリマー , 5種, 1256分子

#2: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Fe / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Fe2S2 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-QKQ / ~{N}-(3-imidazol-1-ylpropyl)-8-(4-methoxyphenyl)-1,6-naphthyridine-2-carboxamide


分子量: 387.434 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C22H21N5O2 / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


分子量: 238.305 Da / 分子数: 12 / 由来タイプ: 天然 / 式: C8H18N2O4S / コメント: pH緩衝剤*YM
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1208 / 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: 2.32 Å3/Da / 溶媒含有率: 46.89 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.6
詳細: 10mM HEPES, 20% PEG3350 (w/v) 0.2M NaSCN, 0.5mM TCEP, 250mM MMV020670
PH範囲: 7.0 - 7.6

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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: Diamond / ビームライン: I24 / 波長: 0.91188 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2019年12月1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: 0.91188 Å / 相対比: 1
反射解像度: 2.01→80.67 Å / Num. obs: 322879 / % possible obs: 99.44 % / 冗長度: 6.9 % / Biso Wilson estimate: 33.1 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.06784 / Rrim(I) all: 0.1787 / Net I/σ(I): 6.88
反射 シェル解像度: 2.01→2.082 Å / 冗長度: 6.8 % / Rmerge(I) obs: 1.783 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 32095 / CC1/2: 0.698 / CC star: 0.907 / Rpim(I) all: 0.7328 / Rrim(I) all: 1.929 / % possible all: 99.07

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PDB_EXTRACT3.25データ抽出
DIALSデータ削減
DIALS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: 6Y9D

6y9d


解像度: 2.01→80.663 Å / SU ML: 0.28 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 33.29 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2546 16241 5.04 %
Rwork0.2139 305750 -
obs0.2159 321991 99.44 %
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: 178.25 Å2 / Biso mean: 51.6225 Å2 / Biso min: 18.93 Å2
精密化ステップサイクル: final / 解像度: 2.01→80.663 Å
タンパク質核酸リガンド溶媒全体
原子数34907 0 792 1208 36907
Biso mean--65.4 44.18 -
残基数----4305
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A12180X-RAY DIFFRACTION3.966TORSIONAL
12B12180X-RAY DIFFRACTION3.966TORSIONAL
13C12180X-RAY DIFFRACTION3.966TORSIONAL
14D12180X-RAY DIFFRACTION3.966TORSIONAL
15E12180X-RAY DIFFRACTION3.966TORSIONAL
16F12180X-RAY DIFFRACTION3.966TORSIONAL
17G12180X-RAY DIFFRACTION3.966TORSIONAL
18H12180X-RAY DIFFRACTION3.966TORSIONAL
19I12180X-RAY DIFFRACTION3.966TORSIONAL
110J12180X-RAY DIFFRACTION3.966TORSIONAL
111K12180X-RAY DIFFRACTION3.966TORSIONAL
112L12180X-RAY DIFFRACTION3.966TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.03280.41955120.39471016399
2.0328-2.05680.41985330.37511009799
2.0568-2.08180.39964590.37041020999
2.0818-2.10820.39275470.3561018599
2.1082-2.13590.37015330.32581012299
2.1359-2.16520.36315190.3121022099
2.1652-2.19610.34285210.30321010399
2.1961-2.22890.34496350.29921012899
2.2289-2.26380.35165600.292510141100
2.2638-2.30090.30835680.28410119100
2.3009-2.34050.3295570.27321020599
2.3405-2.38310.30825010.26431014699
2.3831-2.42890.28595340.25691017999
2.4289-2.47850.29144510.2531027599
2.4785-2.53240.32025180.251110251100
2.5324-2.59130.30324990.244910262100
2.5913-2.65610.30515390.23641011799
2.6561-2.7280.27975290.222610225100
2.728-2.80820.25865430.219510209100
2.8082-2.89890.27985600.230810206100
2.8989-3.00250.2795900.229410173100
3.0025-3.12270.26885630.220410200100
3.1227-3.26480.25255860.202310200100
3.2648-3.4370.24485140.206810244100
3.437-3.65230.23885400.192310215100
3.6523-3.93430.21135660.171410252100
3.9343-4.33020.19756090.150910183100
4.3302-4.95670.17815720.147210175100
4.9567-6.24460.20485400.166710295100
6.2446-80.60.20285430.18041025198
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)
10.7599-0.00460.39740.30190.24021.2606-0.02450.0117-0.06860.0077-0.06180.1215-0.0319-0.33310.00010.25480.0098-0.0040.42010.01650.35167.993518.258335.5097
20.15150.06060.14050.02130.04260.1385-0.36970.07810.6245-0.0996-0.2790.6996-0.67690.07180.00771.0580.0349-0.01041.3192-0.19530.6346-1.271130.741163.5698
30.9951-0.58260.97870.9523-0.3444.2917-0.2092-0.4390.06430.4318-0.02630.7016-0.7611-0.3753-0.84060.27390.00340.25261.1382-0.10070.5065-10.266526.724755.0318
40.65840.03640.42140.45620.07671.5794-0.1287-0.3297-0.00970.1707-0.03630.0911-0.2401-0.5838-0.00010.42640.06330.04730.5629-0.04210.3674.208924.697853.6165
50.6428-0.3662-0.2970.048-0.00481.3347-0.0097-0.04520.1169-0.01790.0351-0.05270.09190.527-0.00280.27590.01740.04480.4812-0.01630.34352.838614.124338.3563
60.52480.48090.20190.23870.25730.3737-0.17050.43530.1808-0.05130.07830.0777-0.0713-0.1413-0.00010.32370.00380.0410.64230.12260.41443.36222.322817.9396
70.876-0.41460.05760.44020.42540.86840.04030.42610.1363-0.14630.0289-0.0631-0.0817-0.034-0.00020.3340.01740.07910.35130.04270.395837.570721.117725.1724
80.7342-0.07510.313-0.15220.0271.87580.046-0.0799-0.01080.1813-0.0077-0.03230.1456-0.2704-0.0040.50830.00020.04330.4213-0.00620.283226.810816.705376.3031
90.1853-0.04780.09390.18980.34150.56080.11760.13860.0160.10280.0609-0.12790.06250.77570.00070.4747-0.0085-0.0220.7102-0.05360.333950.345620.57676.1345
100.37140.3202-0.13650.46910.26920.8730.0575-0.0589-0.01990.14220.04460.06760.02320.52690.00040.45210.03740.00810.5013-0.04930.294747.663520.136468.7261
111.3487-0.06470.3087-0.08740.01821.1762-0.0205-0.0416-0.01710.0423-0.0314-0.00590.07290.25260.00020.29920.0289-0.01680.29740.00620.344737.2689-70.585643.0408
120.17370.087-0.05080.22910.28230.2948-0.04060.4987-0.1275-0.0920.1584-0.1088-0.36640.55210.00450.4393-0.05350.00960.97290.00230.348153.196-63.470120.2853
130.98120.08690.69890.09190.09261.2965-0.07490.37870.070.0344-0.04940.0734-0.18680.3929-0.00060.292-0.0004-0.00720.4210.06670.319141.7314-65.164124.5088
141.34740.02690.3381-0.0357-0.04160.8675-0.0111-0.27520.04440.03560.0569-0.00510.0341-0.2623-0.00010.2768-0.00980.03430.40450.03110.3255-6.8036-70.010741.3687
150.2159-0.31660.22380.4077-0.28420.1697-0.3226-0.44550.18030.27480.5402-0.0216-0.39030.13540.02590.58320.00320.02950.8412-0.09920.45542.9526-61.282967.2448
160.7490.07110.16010.0957-0.230.8923-0.0313-0.45370.18210.02080.0773-0.0889-0.1526-0.1125-0.00010.33660.03340.03380.4961-0.07970.39232.8214-58.777151.5374
170.21830.01320.0750.2984-0.06810.07530.1146-0.6527-0.1130.017-0.0252-0.04780.1515-0.2014-0.00090.3804-0.05460.01340.67070.09020.374412.132-77.227659.0969
180.8698-0.39820.1328-0.22370.08021.50280.02130.2342-0.0245-0.0707-0.01880.04820.15720.3772-0.00330.27960.03450.0060.2363-0.03080.287118.4533-71.70871.9726
190.40290.0330.14990.405-0.34190.66820.02170.1287-0.00590.07540.09010.10870.0397-0.44390.00150.2678-0.00520.01260.38140.02030.3288-6.0134-63.16873.2958
200.2692-0.1316-0.12270.2798-0.12230.90910.03860.072-0.03960.0841-0.02860.00140.0307-0.17650.00010.2557-0.02370.00030.1932-0.02120.2826-1.0524-64.79818.4196
210.67960.06770.0897-0.05220.00121.46480.0187-0.17070.01480.0695-0.0101-0.0167-0.08920.1359-0.00140.2310.0057-0.01740.2938-0.0260.2666-14.0634-21.250753.755
220.5713-0.2648-0.20440.023-0.03130.52090.15560.07050.0541-0.01780.06950.0642-0.1913-0.8650.0870.2211-0.0026-0.04150.6830.01380.2843-40.4261-26.481451.6165
231.0456-0.9025-0.26280.66390.23380.9035-0.21510.15-0.2607-0.22460.32360.38980.4108-0.93180.01480.282-0.1236-0.00910.56850.02940.3872-33.7426-31.023255.7654
240.01390.04630.430.4683-0.12681.43960.0557-0.07710.0135-0.0707-0.0049-0.01590.1432-0.44050.00370.2431-0.0111-0.02920.3555-0.01170.2852-34.3875-27.112946.0787
250.77190.0457-0.1824-0.0253-0.03840.99580.0279-0.05590.0631-0.02410.0052-0.03030.0180.30590.00060.2211-0.0361-0.00490.258-0.00310.28325.3203-20.778212.9792
260.2847-0.1055-0.15290.2610.27750.22790.1277-0.1559-0.00320.0890.0665-0.02470.24030.4810.02550.3070.0758-0.05850.7928-0.04840.313120.8769-28.522535.5027
270.54830.137-0.38490.18580.06141.312-0.0183-0.3470.03670.067-0.02130.06290.15830.3828-0.00140.24890.0283-0.0190.37850.01370.26859.6362-26.870131.2655
281.4980.052-0.6474-0.075-0.18361.1139-0.05210.10160.027-0.01830.04060.0065-0.1321-0.43540.00060.21430.0195-0.03320.37020.02260.2917-40.6902-21.255716.1479
290.38350.3751-0.0030.4137-0.38890.6096-0.2220.97280.0533-0.20970.1007-0.1330.2199-0.1983-0.00760.3152-0.09830.02270.6662-0.02930.2871-28.447-27.257-5.5429
300.4257-0.1834-0.29960.1529-0.11060.6549-0.08460.0665-0.20140.0642-0.04790.02150.2039-0.2368-0.00020.3039-0.08350.04630.2603-0.04510.3595-31.5082-36.36726.3996
310.46870.014-0.02790.4287-0.07080.2018-0.11350.7387-0.00790.07950.0166-0.0744-0.0875-0.21590.00160.2886-0.0014-0.02550.26290.11850.3612-18.8975-18.33830.2637
320.8785-0.17720.29870.0376-0.20411.69010.0245-0.05780.00610.13050.03-0.0133-0.16570.2167-0.00050.3369-0.0291-0.00470.22850.00320.286931.3785-20.9592132.3687
330.3303-0.3135-0.16210.2811-0.06430.50750.0391-0.1031-0.054-0.00850.06530.1656-0.1482-0.94710.01410.272-0.03980.0070.76690.07120.33164.9716-24.2334132.0295
340.45770.09320.54740.3276-0.25741.53140.0817-0.0127-0.05450.00480.049-0.01850.0626-0.32440.00040.2989-0.02-0.00620.30360.02930.294111.8916-25.3191126.4541
350.17070.2795-0.06610.3615-0.47080.88580.06550.02190.04530.0399-0.2330.0866-0.13270.5509-0.03070.3068-0.09530.01350.6662-0.01540.297251.598-19.484698.5933
360.4014-0.0697-0.27720.1773-0.1840.2691-0.03620.2761-0.02840.01090.0072-0.01120.1170.0937-00.3159-0.02060.02440.6358-0.00030.324540.5458-23.527774.4264
370.13130.14180.16140.59830.01390.4594-0.0456-0.26160.1728-0.239-0.2323-0.01050.22221.0271-0.31760.19190.05860.08231.06380.0630.281158.7741-26.311998.123
380.7832-0.5647-1.27930.42880.92862.0765-0.4567-0.0083-0.49750.1959-0.25310.00860.71170.0798-0.19790.45660.0636-0.01361.46380.09080.528962.9613-32.4061118.853
391.35230.1428-0.08480.45990.07930.71280.1436-0.3779-0.0269-0.04180.2969-0.52960.22130.65521.46720.19780.0691-0.06631.67850.08240.41467.9535-31.3245110.3234
400.44220.30490.11420.4191-0.10220.3867-0.1268-0.2734-0.0048-0.01570.04380.00590.26040.8975-0.04280.3580.20040.03570.7860.03040.257355.2438-33.5932101.9396
410.1667-0.06940.06790.2047-0.02730.3003-0.0479-0.18440.2127-0.02180.0548-0.33930.30450.3794-0.00140.4740.09840.06560.54510.04250.314949.2457-37.4998111.7203
420.6595-0.3237-0.19660.7721-0.24380.34170.1452-0.24570.20360.38370.11380.081-0.73421.33010.23780.1631-0.3367-0.12251.2931-0.08810.330357.3162-16.4908117.9862
430.5742-0.1341-0.17880.0328-0.06441.33030.03820.0567-0.0153-0.01830.07890.0538-0.0992-0.35070.00010.278-0.0238-0.04450.50160.08740.33194.9673-19.278694.7083
441.09420.4926-0.18950.6166-0.37690.9099-0.06750.4178-0.1645-0.15570.1107-0.06630.08870.05020.00120.3071-0.0431-0.0250.5071-0.03280.326918.9083-26.320477.9226
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 204 )A3 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 221 )A205 - 221
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 263 )A222 - 263
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 371 )A264 - 371
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 203 )B3 - 203
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 287 )B204 - 287
7X-RAY DIFFRACTION7chain 'B' and (resid 288 through 371 )B288 - 371
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 192 )C3 - 192
9X-RAY DIFFRACTION9chain 'C' and (resid 193 through 287 )C193 - 287
10X-RAY DIFFRACTION10chain 'C' and (resid 288 through 371 )C288 - 371
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 203 )D3 - 203
12X-RAY DIFFRACTION12chain 'D' and (resid 204 through 263 )D204 - 263
13X-RAY DIFFRACTION13chain 'D' and (resid 264 through 371 )D264 - 371
14X-RAY DIFFRACTION14chain 'E' and (resid 3 through 212 )E3 - 212
15X-RAY DIFFRACTION15chain 'E' and (resid 213 through 256 )E213 - 256
16X-RAY DIFFRACTION16chain 'E' and (resid 257 through 335 )E257 - 335
17X-RAY DIFFRACTION17chain 'E' and (resid 336 through 371 )E336 - 371
18X-RAY DIFFRACTION18chain 'F' and (resid 3 through 182 )F3 - 182
19X-RAY DIFFRACTION19chain 'F' and (resid 183 through 263 )F183 - 263
20X-RAY DIFFRACTION20chain 'F' and (resid 264 through 371 )F264 - 371
21X-RAY DIFFRACTION21chain 'G' and (resid 3 through 192 )G3 - 192
22X-RAY DIFFRACTION22chain 'G' and (resid 193 through 240 )G193 - 240
23X-RAY DIFFRACTION23chain 'G' and (resid 241 through 287 )G241 - 287
24X-RAY DIFFRACTION24chain 'G' and (resid 288 through 371 )G288 - 371
25X-RAY DIFFRACTION25chain 'H' and (resid 3 through 203 )H3 - 203
26X-RAY DIFFRACTION26chain 'H' and (resid 204 through 263 )H204 - 263
27X-RAY DIFFRACTION27chain 'H' and (resid 264 through 371 )H264 - 371
28X-RAY DIFFRACTION28chain 'I' and (resid 3 through 192 )I3 - 192
29X-RAY DIFFRACTION29chain 'I' and (resid 193 through 277 )I193 - 277
30X-RAY DIFFRACTION30chain 'I' and (resid 278 through 318 )I278 - 318
31X-RAY DIFFRACTION31chain 'I' and (resid 319 through 371 )I319 - 371
32X-RAY DIFFRACTION32chain 'J' and (resid 3 through 192 )J3 - 192
33X-RAY DIFFRACTION33chain 'J' and (resid 193 through 263 )J193 - 263
34X-RAY DIFFRACTION34chain 'J' and (resid 264 through 371 )J264 - 371
35X-RAY DIFFRACTION35chain 'K' and (resid 3 through 83 )K3 - 83
36X-RAY DIFFRACTION36chain 'K' and (resid 84 through 141 )K84 - 141
37X-RAY DIFFRACTION37chain 'K' and (resid 142 through 203 )K142 - 203
38X-RAY DIFFRACTION38chain 'K' and (resid 204 through 229 )K204 - 229
39X-RAY DIFFRACTION39chain 'K' and (resid 230 through 263 )K230 - 263
40X-RAY DIFFRACTION40chain 'K' and (resid 264 through 305 )K264 - 305
41X-RAY DIFFRACTION41chain 'K' and (resid 306 through 335 )K306 - 335
42X-RAY DIFFRACTION42chain 'K' and (resid 336 through 371 )K336 - 371
43X-RAY DIFFRACTION43chain 'L' and (resid 3 through 192 )L3 - 192
44X-RAY DIFFRACTION44chain 'L' and (resid 193 through 371 )L193 - 371

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万見について

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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://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

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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