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万見

- PDB-6whl: The crystal structure of a beta-lactamase from Legionella pneumop... -

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データを開く

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基本情報

登録情報

データベース: PDB / ID: 6whl

タイトル

The crystal structure of a beta-lactamase from Legionella pneumophila str. Paris

要素

Beta-lactamase

Β-ラクタマーゼ

キーワード

HYDROLASE (加水分解酵素) / beta lactamase /

Structural Genomics (構造ゲノミクス) / Center for Structural Genomics of Infectious Diseases / CSGID

機能・相同性

機能・相同性情報

penicillin binding / antibiotic catabolic process /

beta-lactamase activity /

Β-ラクタマーゼ / response to antibiotic
類似検索 - 分子機能

生物種

Legionella pneumophila (レジオネラ・ニューモフィラ)

手法

X線回折 /

シンクロトロン /

単波長異常分散 / 解像度: 2.3 Å

データ登録者

Tan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

資金援助

米国, 1件

引用

ジャーナル: To Be Published
タイトル: The crystal structure of a beta-lactamase from Legionella pneumophila str. Paris
著者: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A.

履歴

登録	2020年4月8日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年4月22日	Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア	分子: MolmilJmol/JSmol

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ダウンロードとリンク

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ダウンロード

PDBx/mmCIF形式	6whl.cif.gz	1.4 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6whl.ent.gz	1 MB	表示	PDB形式
PDBx/mmJSON形式	6whl.json.gz		ツリー表示	PDBx/mmJSON形式
その他	その他のダウンロード

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検証レポート

アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/wh/6whl ftp://data.pdbj.org/pub/pdb/validation_reports/wh/6whl	HTTPS FTP

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関連構造データ

類似構造データ	6zrn-2 4fd7-3 4fd7-1 1x8m-1 1x8m-5 4oze-2 1x8m-6 2go3-2 6zqt-1 3ho6-1 Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) 類似検索 - 機能・相同性F&H 検索類似検索 - 機能F&H 検索類似検索 - 相同性F&H 検索
その他のデータベース	TargetTrack: IDP97258

類似構造データ

Omokage検索で類似形状データを探す (詳細)

その他のデータベース

TargetTrack: IDP97258

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リンク

PDBのページ	PDBj / wwPDB / NCBI

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集合体

登録構造単位

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

E: Beta-lactamase

F: Beta-lactamase

G: Beta-lactamase

H: Beta-lactamase

I: Beta-lactamase

J: Beta-lactamase

K: Beta-lactamase

L: Beta-lactamase

ヘテロ分子

351 kDa, 12 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

A: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

B: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

C: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.3 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

D: Beta-lactamase

登録者が定義した集合体
29.1 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

E: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

F: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

G: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

H: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

I: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

J: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

K: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

L: Beta-lactamase

ヘテロ分子

登録者が定義した集合体
29.2 kDa, 1 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

単位格子

Length a, b, c (Å)	80.222, 178.196, 143.749
Angle α, β, γ (deg.)	90.000, 97.038, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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要素

#1: タンパク質	Beta-lactamase / Β-ラクタマーゼ分子量: 29132.418 Da / 分子数: 12 / 由来タイプ: 組換発現由来: (組換発現) Legionella pneumophila (レジオネラ・ニューモフィラ) 株: Paris / 遺伝子: bla, NCTC12000_01749 / プラスミド: pMCSG53 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3) 参照: UniProt: A0A378KDC5, UniProt: A0A3A6V665*PLUS, Β-ラクタマーゼ
#2: 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: 12 / 由来タイプ: 合成 / 式: C₃H₈O₃
#3: 水	ChemComp-HOH / water / 水分子量: 18.015 Da / 分子数: 529 / 由来タイプ: 天然 / 式: H₂O
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: 2.94 Å³/Da / 溶媒含有率: 58.1 %
結晶化	温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.2M ammonium tartrate dibasic, 20% (w/v) PEG 3350

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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: APS / ビームライン: 19-ID / 波長: 0.97918 Å
検出器	タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2018年11月13日
放射	モノクロメーター: Si 111 / 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: 0.97918 Å / 相対比: 1
反射	解像度: 2.3→42.6 Å / Num. obs: 176499 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 3.1 % / B_iso Wilson estimate: 29.96 Å² / CC_1/2: 0.991 / CC star: 0.998 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.037 / R_rim(I) all: 0.068 / Χ²: 0.708 / Net I/σ(I): 15.96
反射シェル	解像度: 2.3→2.34 Å / 冗長度: 3.1 % / R_merge(I) obs: 0.842 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 8765 / CC_1/2: 0.551 / CC star: 0.843 / R_pim(I) all: 0.56 / R_rim(I) all: 1.014 / Χ²: 0.884 / % possible all: 98.9

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解析

ソフトウェア

名称	バージョン	分類
SBC-Collect		データ収集
PHENIX	1.17.1_3660	精密化
HKL-3000		データスケーリング
HKL-3000		データ削減
HKL-3000		位相決定

精密化

構造決定の手法:

単波長異常分散 / 解像度: 2.3→42.52 Å / SU ML: 0.2579 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.2908

	R_factor	反射数	%反射	Selection details
R_free	0.2081	7619	4.89 %	random
R_work	0.1634	-	-	-
obs	0.1655	155665	87.87 %	-

溶媒の処理

減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å

原子変位パラメータ

B_iso mean: 39.62 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.3→42.52 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	24048	0	72	529	24649

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0074	24744
X-RAY DIFFRACTION	f_angle_d	0.8949	33447
X-RAY DIFFRACTION	f_chiral_restr	0.047	3504
X-RAY DIFFRACTION	f_plane_restr	0.0053	4227
X-RAY DIFFRACTION	f_dihedral_angle_d	18.2404	9069

LS精密化シェル

解像度 (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.33	0.2779	113	0.2207	2405	X-RAY DIFFRACTION	43.11
2.33-2.35	0.2989	145	0.229	2798	X-RAY DIFFRACTION	49.86
2.35-2.38	0.3037	160	0.2232	3112	X-RAY DIFFRACTION	55.84
2.38-2.41	0.2668	170	0.2183	3333	X-RAY DIFFRACTION	59.44
2.41-2.44	0.2798	168	0.2101	3506	X-RAY DIFFRACTION	62.41
2.44-2.48	0.2506	214	0.2233	3677	X-RAY DIFFRACTION	65.76
2.48-2.51	0.2879	191	0.2263	3926	X-RAY DIFFRACTION	69.47
2.51-2.55	0.2714	185	0.2156	4120	X-RAY DIFFRACTION	73.99
2.55-2.59	0.2711	241	0.2122	4843	X-RAY DIFFRACTION	85.49
2.59-2.63	0.2642	292	0.2142	5306	X-RAY DIFFRACTION	95.84
2.63-2.68	0.2414	302	0.2101	5513	X-RAY DIFFRACTION	97.9
2.68-2.73	0.2464	289	0.1955	5501	X-RAY DIFFRACTION	98.72
2.73-2.78	0.2553	318	0.1945	5511	X-RAY DIFFRACTION	98.78
2.78-2.84	0.2445	277	0.1947	5533	X-RAY DIFFRACTION	98.79
2.84-2.9	0.2543	274	0.1991	5539	X-RAY DIFFRACTION	98.89
2.9-2.97	0.2537	306	0.1897	5615	X-RAY DIFFRACTION	99.13
2.97-3.04	0.2679	290	0.1838	5465	X-RAY DIFFRACTION	98.41
3.04-3.12	0.2203	282	0.1897	5439	X-RAY DIFFRACTION	96.8
3.12-3.21	0.2305	278	0.1823	5584	X-RAY DIFFRACTION	99.15
3.21-3.32	0.2249	286	0.1828	5591	X-RAY DIFFRACTION	99.53
3.32-3.44	0.2185	270	0.1734	5557	X-RAY DIFFRACTION	99.39
3.44-3.57	0.193	295	0.1571	5579	X-RAY DIFFRACTION	99.21
3.57-3.74	0.2	304	0.1474	5552	X-RAY DIFFRACTION	99.1
3.74-3.93	0.178	258	0.1386	5577	X-RAY DIFFRACTION	98.9
3.93-4.18	0.1744	308	0.1317	5488	X-RAY DIFFRACTION	97.69
4.18-4.5	0.155	304	0.1168	5621	X-RAY DIFFRACTION	99.73
4.5-4.95	0.1545	285	0.1138	5588	X-RAY DIFFRACTION	99.44
4.95-5.67	0.165	263	0.1289	5593	X-RAY DIFFRACTION	98.52
5.67-7.14	0.1967	269	0.1518	5570	X-RAY DIFFRACTION	98.18
7.14-42.52	0.1644	282	0.1469	5604	X-RAY DIFFRACTION	97.61

精密化 TLS

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

ID	L11 (°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)
1	8.16521654214	-2.02471243551	-1.23384516595	3.88166856109	0.255964847611	2.5393277682	0.119748889351	0.51792015568	-0.154631612434	-0.276307577986	0.0193593977657	0.260268990281	0.194517351201	-0.088027267024	-0.130647601678	0.206043327576	-0.018112839163	-0.0577809583481	0.141669858273	0.0100878335435	0.127585375466	7.01456106998	39.7788312862	85.0646363169
2	4.58752041006	6.23746626934	1.38029943598	9.03532286548	1.24187354397	6.99441736127	-0.124897876663	0.727859178264	-0.312243528867	-0.775939629178	0.223389406261	-0.418734376509	0.117010286684	0.799387878889	-0.119217905422	0.432723744735	0.17199648418	0.13505543096	0.47765817232	0.020762545252	0.310882602703	21.7636325618	47.8687454905	63.0525700884
3	1.57562576956	2.00973089046	1.1231786716	3.24389827184	0.034165191371	3.67605339643	0.0504916672078	0.223152968179	-0.0685795663875	-0.50022250476	0.133206888203	-0.0650570940376	0.0120529032315	0.323428037319	-0.145236256545	0.436615256779	0.0412021060199	-0.0205041516554	0.188805157689	0.0335740893028	0.14222289049	6.27838246845	53.8392340035	64.5132223453
4	4.14325580958	0.0396382832552	-0.502070795024	6.57353068262	-2.81880298912	2.72464105358	0.0154572600071	-0.130204133527	-0.124407208597	0.0774071835601	0.153401790104	0.561172900093	-0.327060761436	-0.437352260734	-0.146666301269	0.251256063172	0.0614569275399	0.0313167362252	0.153964681461	0.00914761997177	0.177720808226	-3.62853293096	58.0349241537	79.9737836357
5	1.97037623228	-0.870207440227	-0.719546048398	2.00130731155	-0.477895167608	2.29660433674	0.19201205213	0.216238019388	0.0954764724806	-0.537548356162	-0.143562129101	0.106641789829	-0.185218310405	0.0012719264111	-0.0611699497982	0.424951677507	0.0501717528381	-0.00556535008719	0.123295660758	0.00224642357905	0.157574798453	2.67815022485	60.0886907572	64.2018107827
6	1.42621187048	-0.141312298927	-0.529333414928	1.6676792746	0.294393142804	1.83178626848	0.220575873265	-0.0378839076696	-0.00427398338626	-0.486769525773	-0.232834702039	0.264098476492	0.102716510199	-0.10686728525	-0.0033357073373	0.422993555686	0.0388038848952	-0.0557532664325	0.124056190186	0.00627165015812	0.148309410883	8.48873331929	49.0524865192	71.4312289623
7	5.26323383277	0.714438891539	0.581615868841	2.59141131227	0.541949539387	3.70555434529	0.0907205094726	-0.141879173733	-0.272851062898	-0.429895073233	-0.0741691043375	-0.230524945554	0.188169190929	0.345585517282	-0.0467866633902	0.32745614547	0.0579419376068	0.0421032626848	0.157223684553	0.0125354552263	0.130972035449	16.6632017719	46.0676974744	71.9738526251
8	6.06756448358	-3.97259129669	5.49576618745	3.91918579577	-6.13962394386	9.88692088025	-0.0471029746105	0.101065322762	0.216216139024	-0.222858128287	0.0346955189347	0.104282388819	0.0829629840437	0.0154485884829	-0.0239332140377	0.261433556376	-0.104229925817	-0.0561330542001	0.209688003191	-0.0136016487532	0.253879372747	-1.59478692025	27.1171824434	94.8843180112
9	1.64160409276	0.726502358817	0.0513305003176	4.43115630145	-0.629904755992	2.22773925034	-0.183908497093	0.0940115040371	0.0716626006009	0.057994269376	0.025122239919	0.237694009826	-0.113249789096	-0.456260678016	0.166517169567	0.0932482768554	0.040378341921	-0.00989129596204	0.229393768586	-0.0372770111858	0.258383671127	-23.9868434791	16.4958871838	97.3553898205
10	2.71939418558	-0.00712457297585	0.140886896373	2.8974025873	0.364546234065	2.41686834283	-0.199508188316	0.106640441178	0.0656825349362	0.124891641754	-0.0996043713215	0.450870527671	-0.00329861443706	-0.537842805492	0.257710393638	0.101988116587	-0.00774803905247	0.00428852701	0.254292871776	-0.0306923063037	0.266012777933	-27.5669898655	14.3439760967	96.1007820247
11	2.45095228323	-0.0986050970931	-0.765217685505	1.64501377922	-0.00847467440103	1.6634916177	-0.0262361503125	0.0984907025281	0.201134358387	-0.122016132337	-0.0572734415288	0.189411838347	-0.270592379295	-0.184483802236	0.0474051979972	0.198421026456	0.0141731685122	-0.0646220297615	0.0885279277921	-0.0153543038056	0.185008539696	-15.434390807	21.7343662008	95.3385241929
12	4.21369054318	-2.14064000199	5.37872910052	2.8688740087	-1.50209091764	7.71466077397	-0.183028195255	0.400444105009	0.162863809346	0.0366743830631	-0.00467054290764	-0.370916369588	-0.311945567107	0.331550973667	0.202137337585	0.134313149329	-0.0126119921899	0.0145589291019	0.158756715802	0.0240762703481	0.191436434753	-0.225033918646	16.375568055	89.4415664716
13	9.09584172352	5.38502536663	-3.96138163475	7.74403344883	-2.30757279164	6.21433867241	-0.093404525868	0.273919247612	0.195571908574	-0.408693232741	-0.0135079177621	0.171845543578	-0.130889093641	0.291697506703	0.0271151998116	0.485808056317	-0.0382606019595	0.00672932619893	0.184237095035	0.0218405604137	0.166157103979	-10.4570871773	-1.49034957149	70.4941414269
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49	5.40239641791	-7.05937487358	4.92318832278	9.22760554803	-6.43537284683	4.49045963521	-0.0442570511027	-0.415438792783	-0.0233147621368	0.242742661489	0.1986581623	-0.00673256284681	-0.0111913645096	-0.316993465828	-0.218750414174	0.396478353565	0.0255034157763	0.00200978584882	0.401453432802	-0.00131456522384	0.228800399209	-9.02692549324	85.9284189787	144.153180128
50	2.48573988363	0.230243161793	-0.320602289965	2.53188033513	-0.364458720513	3.75118095837	0.0564658239771	-0.282539587347	0.160184232382	0.216194831618	0.0487243581815	-0.0611197541123	-0.617311167492	0.0139981897569	-0.0867485225092	0.429395543093	-0.0412637331375	-0.0894094584398	0.2149432857	-0.0248338963231	0.237527563179	6.29827357681	91.2225969201	141.084606033
51	4.0048979065	-0.247646526066	-0.37990577278	3.84095848174	-0.124713505784	3.13908010848	-0.173441188332	0.0443976948977	-0.00029485883046	-0.240951452302	-0.0264040433306	-0.69109066568	-0.517432035867	0.507509808879	0.192815536989	0.466950952161	-0.232120491931	0.0112187362705	0.356465758982	0.0929226142638	0.460915103772	18.7571988618	93.3606544555	125.058092481
52	2.55261071861	-0.017777724229	-0.503469054327	3.04916244877	0.192792779392	2.02612952863	-0.183444622653	-0.124966148639	0.0495425696962	0.0379827518277	0.101846427224	-0.44615463734	-0.59435784014	0.429677651319	0.0267790484384	0.376063938466	-0.1746787498	-0.0378027640632	0.3097411434	0.0310828804766	0.36185107595	16.3588611444	91.7214072026	131.449873626
53	2.53173754362	0.731686495816	-0.186013752908	2.28787515754	0.105647019366	1.965177741	-0.0536452037948	-0.156591125577	0.321872054333	0.1592255603	0.0318274217435	-0.188551710474	-0.597525221996	0.0619680304038	0.0496631907768	0.439853098677	-0.0126251503885	-0.05680952482	0.203539350905	0.00620156131677	0.22113610967	4.73416021255	94.2856754814	137.140972115
54	5.77964385726	0.135046497236	1.39577525971	3.86842044162	-0.0589299433903	5.43134604657	0.0616759896542	-0.285058953607	-0.00364542508276	0.237875456076	0.0778257238579	-0.485624290066	-0.199083550692	0.289818988825	-0.103877376054	0.276808919726	-0.0107707416823	0.0108476159968	0.182008448921	-0.0245132710651	0.150415550987	3.85570980194	82.5391593501	140.85230923
55	2.40856534367	0.226235702082	3.57057928058	2.95074093555	0.317301737259	5.31322025764	0.283171596669	-0.379431363568	-0.60670785519	0.17419417531	-0.119337057033	0.039320872225	0.0949149609439	-0.445414512264	-0.159804424037	0.342903213117	-0.0448793734029	-0.0113829628123	0.248571484818	0.0575808087526	0.217817614417	-7.41300012241	77.6683983283	135.360341095
56	8.21452695015	2.41868966661	-5.61875285142	7.47123277718	-2.40596938998	6.47472924862	0.101443817032	-0.0774387031732	-0.294439605336	0.119972322467	-0.0305108824842	0.12170202618	-0.0369964746852	0.265201669662	-0.033334898918	0.0768227580507	0.0381537427323	-0.0424138785987	0.348381004789	0.0291684238235	0.284911825285	9.50645819448	58.6055355214	123.068369791
57	0.7932052428	-0.0692480818431	-0.737825473308	2.21270889734	-0.504560454615	1.38295442025	0.0198181626725	-0.151505523602	-0.56376407776	-0.152436327763	0.112545663814	-0.0183529833097	0.161830036667	-0.182415495508	-0.0746429249375	0.123518031789	-0.0349803073335	-0.0251386569606	0.252590833971	0.0416615964715	0.438548519895	-6.23313704746	59.4399090819	117.71661093
58	4.7705205515	-1.21779666243	-1.19261013536	2.42488386947	0.99667305826	1.29297739564	0.11594774088	-0.0298558540243	-0.372148275883	-0.332104452997	-0.135774578316	0.586652241841	-0.198144425121	-0.617826777347	-0.002228572613	0.249099763011	0.108477762818	-0.12932382542	0.507674493897	0.0431020904806	0.37710777033	-18.5972321223	74.0682216395	110.64023286
59	4.16865047841	-0.887546040754	0.077372001797	2.68969135994	0.188628573918	2.88015561451	0.156447431895	0.036594316499	-0.48895067085	-0.224410646999	0.012277462245	0.414167156807	0.0208446315918	-0.678762486028	-0.0796482661333	0.15977674195	0.0413245547886	-0.0958099101842	0.393279090062	0.071963714461	0.370490150337	-16.6537317406	68.1132691732	114.744838427
60	1.1127488141	0.586358149985	-0.112921633655	1.75406749019	0.0326199377564	2.55627498241	0.0946960394667	0.101841282391	-0.559095955189	-0.186473553099	0.110316162731	0.189015513485	0.249687109389	-0.424741450803	-0.0121580874272	0.155887347239	-0.017451735474	-0.0403949424259	0.274930552062	0.0239586451256	0.463892666951	-6.68416196432	59.0362883942	112.419602129
61	1.3566905758	-0.0649054626878	-0.831319582958	0.959099060441	-0.333204200674	3.55762772401	-0.0972730391154	-0.0988731809662	-0.577303147786	-0.0846378977073	0.097520585988	0.211124860584	0.10735905479	-0.443479891848	0.0147839342239	0.107987221718	-0.000455703981805	-0.0377685952039	0.271448076091	0.105025290361	0.42981731969	-5.03821689165	65.2773061595	123.677283433
62	3.70925527387	0.785302330568	-0.0933146976902	4.19476865564	0.117065010914	2.45061751619	-0.122707338989	-0.259133679118	0.0774967579472	0.00595833531753	0.0302335269205	0.289057864499	-0.125874644711	-0.0999788589558	0.0560823766725	0.0661304136201	-0.0298577731917	-0.0303587663031	0.239076644484	0.075767525413	0.254257196372	0.414288574029	64.6566194383	125.352460265
63	3.7934092803	3.40712444396	-3.28021074662	4.44754683398	-1.4410160345	4.46913925107	-0.0418729116893	-0.284294625198	-0.139118788919	0.109329428285	0.0771481392937	-0.243334079258	0.0328751119284	0.0606631810549	-0.016897888189	0.197166050821	-0.0772851379011	-0.0540787229764	0.290296306313	0.0721446298428	0.25666469936	7.76688499471	69.3582550262	128.664703016
64	8.11837316173	1.48171573983	1.78375058865	3.0346201674	2.36610323265	4.63552508955	0.0622559833794	0.0334868635893	0.281697977872	0.0105809198614	-0.0662179093613	-0.00226072966782	-0.0899928647395	0.205170748073	-0.0882571229285	0.117674340679	0.0260087509769	0.0262071197794	0.329764562072	-0.0197410789697	0.213599001527	17.4674021829	54.0817427743	126.602184143
65	1.80614521395	-0.777904479143	0.184961996244	2.06120719219	-0.00857297595256	1.00837826796	-0.172345396243	-0.177184320689	0.078607359605	0.168153769072	0.167040630036	-0.279019745145	0.209911450426	0.608358708562	-0.00448863070892	0.115978640821	0.112760281357	-0.0292975244059	0.641191126792	-0.10184443375	0.387734661616	40.1755882454	45.1239529945	131.323758325
66	0.775956272361	-0.277566620479	0.249335466557	0.34206975107	-0.0397189731428	0.147394462385	-0.131696044227	-0.180569234374	0.131965940206	0.134750072854	0.215913886368	-0.198323697168	0.0376361665612	0.375416875282	0.114714720859	0.0114704003136	0.201336185461	-0.113428368014	0.910497502005	-0.152566584641	0.41194700892	43.6357436849	44.2982562316	133.771156618
67	3.08297977839	-0.244868553922	-0.0821486537543	1.95661823694	-0.927022543261	0.687713668763	0.0584551738664	-0.27389585501	0.364748095028	0.289215378926	-0.0346319543239	-0.529597626939	-0.246578045283	0.457752895345	0.127421577955	0.122883778296	-0.136949194516	-0.0306418848594	0.713969215184	-0.103973023646	0.466834272525	43.9905859171	57.0038151924	125.817486865
68	1.45176795048	-0.325690043481	-0.0127698150538	0.630634836841	-0.169631429821	0.898704460643	-0.0249915187652	0.00854375760953	-0.149079001505	0.143524555632	0.0715123891832	-0.0745102281725	0.190650327439	0.498803074986	-0.0141747892905	0.117064757847	0.0342065825202	-0.0148273151227	0.406525122511	-0.0897476813495	0.272930633338	29.8124148486	43.9074494031	125.841184656
69	5.47510202077	4.1554934679	0.675384884016	8.24909199301	0.828715815514	2.85833409971	-0.155478229828	-0.193550726409	0.228327607236	0.00852345527274	0.23549351575	-0.527127641378	-0.509309084815	0.854383845843	-0.0645100275106	0.232405311885	-0.0235990560549	-0.0133502339675	0.499907006895	-0.137977507963	0.300052633028	34.4610658629	58.1706302491	135.470266516
70	4.22744386149	1.02096653702	-0.322815531623	5.05186641299	-0.563846195317	1.51623405884	-0.0430041719985	-0.281344571558	-0.0121380106739	0.486218076713	0.0907883001827	-0.142424325869	0.0097155482751	0.300949154244	-0.0619663674677	0.114838102426	0.0335769308734	0.0197628358389	0.312729181177	-0.0826020615416	0.199701127051	24.4042127436	50.7501756691	134.247923653
71	8.63944179143	5.33340669321	1.92678328829	6.56807839312	2.14966048264	4.32716230524	-0.254931873563	-0.613253375937	0.333543011372	0.110415570779	0.0532202008166	0.364481077396	0.0107167726922	0.00610778423818	0.143212507941	0.142281352167	0.0318032381547	0.0651197547289	0.228848444567	-0.0327620730095	0.226073961367	15.8312374247	47.5615150876	136.437688051
72	7.95791351377	-1.8916935682	-0.0961127178596	6.20988237333	2.74365023973	7.86587475345	-0.319808605818	-1.00521675893	0.0732118841988	1.08143082667	0.244509545536	0.0404941143995	0.242689541853	0.279882208597	0.0310532867759	0.63457094137	0.248845164806	0.0012520328382	0.749303571975	-0.0217828873449	0.334239923739	24.1515253015	43.6689909693	162.431264815
73	1.13394290154	0.17459469228	0.207441650861	1.66439159422	-0.398183424539	2.00503990015	-0.32713591678	-0.286913423362	-0.712278707271	0.469257890542	0.235398793882	0.406928713456	0.938852025233	-0.310548502264	-0.0305834291435	0.700512021596	0.0320553379788	0.245732061156	0.351374722265	0.123753002077	0.657329588339	5.28908329985	29.7420216966	150.067198829
74	1.10150914428	-0.299115372885	0.604655013817	1.01989306285	0.207146512399	0.698662928155	-0.185850048681	-0.477605078732	-0.69703407238	0.578921247277	0.217228001331	0.198977420948	0.752909203995	0.196171575934	-0.0438090880838	0.758641765876	0.306287527867	0.154815643095	0.452036593948	0.124763847413	0.493948772136	16.0641462276	31.5579859928	154.273673986
75	0.737848959596	0.744296648687	0.613536135276	0.824696359548	0.428385973526	1.03827625407	-0.31452235668	-0.44853441517	-0.252645111374	0.421077003036	0.0752558365376	0.293281315004	0.37558883106	-0.047371781895	0.22998118802	0.409230513947	0.264585526434	0.215234088021	0.418512847868	0.0689256154947	0.312883303993	8.38001938046	43.7057403621	155.881110327
76	5.07988079738	0.499729387489	-0.0353578722271	1.84526134621	-0.0589433557066	2.00738760216	-0.072788851342	-0.108606094624	-0.156927631295	0.35885925208	0.177336599552	-0.0550592039827	0.0872759400986	0.503792674854	-0.0986636098335	0.490872405367	0.257362541614	0.0331810703266	0.455585195676	-0.00589336441364	0.259934658328	22.5529912707	44.9550247974	152.070740375
77	5.6451489108	-3.21129827347	-1.88955461664	7.46578554453	-0.807388940411	5.04903858412	0.0912798658664	0.0346378948948	-0.403021589904	-0.26279046852	-0.0730943632056	0.334889012122	0.520297757308	-0.331446325659	0.071940196283	0.125422399988	-0.0936856527288	-0.0915736905094	0.20422994177	-0.0121061603998	0.231839454457	6.16202417931	32.7818842897	94.9584383774
78	2.56533040338	-0.0671446207459	-0.334331844039	3.13926856394	-0.289578191952	2.29460878564	-0.0371889361712	-0.0601016479565	-0.270089222595	0.0669469320805	0.201254304841	-0.062154137271	0.301264466214	0.346560261835	-0.117877268901	0.134815694066	0.0776153248479	-0.0302189798021	0.219698479723	-0.000285944232919	0.196772385789	22.3901624804	35.8621618791	97.7612063492
79	3.36453832766	0.377265687372	-0.106564020473	1.97498061846	-0.660473900815	1.23265410883	-0.0814717906473	0.320775025614	0.261691848756	-0.058204574029	0.0766984839151	-0.496199384125	-0.231331415062	0.726290644032	-0.044670841384	0.218833662781	-0.1512986835	-0.0733180115481	0.510948506423	-0.133053501769	0.421038684571	35.0581472697	51.6554955791	96.1075658489
80	4.45618894254	0.339992857663	-1.63352248107	2.45601299392	-0.410358772614	2.96476572473	-0.0746646466075	0.48742541912	0.233895537847	-0.426290357213	0.130601004993	-0.449191230031	-0.271670013118	0.654533738738	-0.137216443351	0.200475605227	-0.101921827071	0.0316027661757	0.490309801575	-0.000316645568216	0.284458201757	31.4595404467	48.5689937943	87.3981120624
81	1.31017240821	-0.0052967013074	-0.0535992673049	0.322129226495	-0.253557333079	0.998576438393	-0.0407797152175	-0.0967031745902	0.0213289239614	0.0541701489796	0.0503467661125	-0.24293729917	0.0489229457497	0.487358417707	0.0345788726506	0.0642290247061	0.044117205781	-0.0322424891248	0.523131608778	-0.137087362626	0.318209228214	33.7448815652	41.5593720925	103.570404925
82	2.2966457798	0.0610144761124	0.292024790957	1.04418658303	-0.325060757084	1.19676122029	0.010156648805	-0.0854240667574	0.00342727835	0.0201403117699	0.131139183095	-0.231949607265	0.241143464006	0.445735283188	-0.0840596761584	0.166445115856	0.0572948070639	-0.0330443683438	0.260839433596	-0.0765398319706	0.20250314874	23.4895783693	37.7368865898	102.550041771
83	2.75904060031	0.466455832734	0.0494238663469	1.18337028618	0.0476772101368	1.1946664431	-0.105146817255	0.164801822235	0.401545630987	-0.168977126255	0.0980314168116	-0.0454678576925	-0.178395170458	0.113895858852	-0.0155818911593	0.197750241664	-0.0281153164059	-0.0275829545382	0.124022120722	-0.0102866017257	0.188872751367	11.6488386391	50.4347158988	90.374727655
84	7.63606684096	-2.86218205103	-0.845275742588	5.62027241777	0.901455329536	2.73257481705	-0.0191899325415	-0.213398329442	-0.557400532382	0.16636939647	0.194894064033	-0.713442692614	0.569918715885	0.614815888533	-0.145833018521	0.336447914792	0.0689189992189	-0.0587483128234	0.315142360808	-0.000970065514259	0.211448576661	25.5631314308	31.2294298021	89.7482058109
85	4.46301072834	-0.451011012951	-0.960982410772	3.61469602178	0.453430895282	2.51048901398	0.121231776425	0.177204852134	0.0216154857376	-0.162591506846	0.058242324258	-0.207539730167	0.283852487904	0.0662683699621	-0.103285904207	0.215250279821	0.0219353330369	-0.0419191364814	0.130275150849	-0.028134811386	0.0741252577448	15.0465991841	36.9979464679	89.2291760296

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'G' and (resid 245 through 266 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 21 through 38 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 39 through 60 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 61 through 100 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 101 through 179 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 180 through 213 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 214 through 266 )
8	X-RAY DIFFRACTION	8	chain 'I' and (resid 21 through 38 )
9	X-RAY DIFFRACTION	9	chain 'I' and (resid 39 through 80 )
10	X-RAY DIFFRACTION	10	chain 'I' and (resid 81 through 122 )
11	X-RAY DIFFRACTION	11	chain 'I' and (resid 123 through 244 )
12	X-RAY DIFFRACTION	12	chain 'I' and (resid 245 through 266 )
13	X-RAY DIFFRACTION	13	chain 'J' and (resid 21 through 38 )
14	X-RAY DIFFRACTION	14	chain 'J' and (resid 39 through 60 )
15	X-RAY DIFFRACTION	15	chain 'J' and (resid 61 through 100 )
16	X-RAY DIFFRACTION	16	chain 'J' and (resid 101 through 164 )
17	X-RAY DIFFRACTION	17	chain 'J' and (resid 165 through 191 )
18	X-RAY DIFFRACTION	18	chain 'J' and (resid 192 through 213 )
19	X-RAY DIFFRACTION	19	chain 'J' and (resid 214 through 244 )
20	X-RAY DIFFRACTION	20	chain 'J' and (resid 245 through 266 )
21	X-RAY DIFFRACTION	21	chain 'K' and (resid 21 through 38 )
22	X-RAY DIFFRACTION	22	chain 'K' and (resid 39 through 60 )
23	X-RAY DIFFRACTION	23	chain 'K' and (resid 61 through 80 )
24	X-RAY DIFFRACTION	24	chain 'K' and (resid 81 through 100 )
25	X-RAY DIFFRACTION	25	chain 'K' and (resid 101 through 171 )
26	X-RAY DIFFRACTION	26	chain 'K' and (resid 172 through 201 )
27	X-RAY DIFFRACTION	27	chain 'K' and (resid 202 through 244 )
28	X-RAY DIFFRACTION	28	chain 'K' and (resid 245 through 266 )
29	X-RAY DIFFRACTION	29	chain 'L' and (resid 21 through 38 )
30	X-RAY DIFFRACTION	30	chain 'L' and (resid 39 through 60 )
31	X-RAY DIFFRACTION	31	chain 'L' and (resid 61 through 80 )
32	X-RAY DIFFRACTION	32	chain 'L' and (resid 81 through 100 )
33	X-RAY DIFFRACTION	33	chain 'L' and (resid 101 through 152 )
34	X-RAY DIFFRACTION	34	chain 'L' and (resid 153 through 244 )
35	X-RAY DIFFRACTION	35	chain 'L' and (resid 245 through 266 )
36	X-RAY DIFFRACTION	36	chain 'A' and (resid 21 through 38 )
37	X-RAY DIFFRACTION	37	chain 'A' and (resid 39 through 60 )
38	X-RAY DIFFRACTION	38	chain 'A' and (resid 61 through 80 )
39	X-RAY DIFFRACTION	39	chain 'A' and (resid 81 through 122 )
40	X-RAY DIFFRACTION	40	chain 'A' and (resid 123 through 179 )
41	X-RAY DIFFRACTION	41	chain 'A' and (resid 180 through 213 )
42	X-RAY DIFFRACTION	42	chain 'A' and (resid 214 through 266 )
43	X-RAY DIFFRACTION	43	chain 'B' and (resid 21 through 38 )
44	X-RAY DIFFRACTION	44	chain 'B' and (resid 39 through 80 )
45	X-RAY DIFFRACTION	45	chain 'B' and (resid 81 through 122 )
46	X-RAY DIFFRACTION	46	chain 'B' and (resid 123 through 191 )
47	X-RAY DIFFRACTION	47	chain 'B' and (resid 192 through 244 )
48	X-RAY DIFFRACTION	48	chain 'B' and (resid 245 through 266 )
49	X-RAY DIFFRACTION	49	chain 'C' and (resid 21 through 38 )
50	X-RAY DIFFRACTION	50	chain 'C' and (resid 39 through 60 )
51	X-RAY DIFFRACTION	51	chain 'C' and (resid 61 through 80 )
52	X-RAY DIFFRACTION	52	chain 'C' and (resid 81 through 122 )
53	X-RAY DIFFRACTION	53	chain 'C' and (resid 123 through 191 )
54	X-RAY DIFFRACTION	54	chain 'C' and (resid 192 through 244 )
55	X-RAY DIFFRACTION	55	chain 'C' and (resid 245 through 266 )
56	X-RAY DIFFRACTION	56	chain 'D' and (resid 21 through 38 )
57	X-RAY DIFFRACTION	57	chain 'D' and (resid 39 through 60 )
58	X-RAY DIFFRACTION	58	chain 'D' and (resid 61 through 80 )
59	X-RAY DIFFRACTION	59	chain 'D' and (resid 81 through 122 )
60	X-RAY DIFFRACTION	60	chain 'D' and (resid 123 through 179 )
61	X-RAY DIFFRACTION	61	chain 'D' and (resid 180 through 213 )
62	X-RAY DIFFRACTION	62	chain 'D' and (resid 214 through 244 )
63	X-RAY DIFFRACTION	63	chain 'D' and (resid 245 through 266 )
64	X-RAY DIFFRACTION	64	chain 'E' and (resid 21 through 38 )
65	X-RAY DIFFRACTION	65	chain 'E' and (resid 39 through 80 )
66	X-RAY DIFFRACTION	66	chain 'E' and (resid 81 through 122 )
67	X-RAY DIFFRACTION	67	chain 'E' and (resid 123 through 142 )
68	X-RAY DIFFRACTION	68	chain 'E' and (resid 143 through 191 )
69	X-RAY DIFFRACTION	69	chain 'E' and (resid 192 through 213 )
70	X-RAY DIFFRACTION	70	chain 'E' and (resid 214 through 244 )
71	X-RAY DIFFRACTION	71	chain 'E' and (resid 245 through 266 )
72	X-RAY DIFFRACTION	72	chain 'F' and (resid 21 through 38 )
73	X-RAY DIFFRACTION	73	chain 'F' and (resid 39 through 137 )
74	X-RAY DIFFRACTION	74	chain 'F' and (resid 138 through 201 )
75	X-RAY DIFFRACTION	75	chain 'F' and (resid 202 through 224 )
76	X-RAY DIFFRACTION	76	chain 'F' and (resid 225 through 266 )
77	X-RAY DIFFRACTION	77	chain 'G' and (resid 21 through 38 )
78	X-RAY DIFFRACTION	78	chain 'G' and (resid 39 through 60 )
79	X-RAY DIFFRACTION	79	chain 'G' and (resid 61 through 80 )
80	X-RAY DIFFRACTION	80	chain 'G' and (resid 81 through 100 )
81	X-RAY DIFFRACTION	81	chain 'G' and (resid 101 through 122 )
82	X-RAY DIFFRACTION	82	chain 'G' and (resid 123 through 179 )
83	X-RAY DIFFRACTION	83	chain 'G' and (resid 180 through 191 )
84	X-RAY DIFFRACTION	84	chain 'G' and (resid 192 through 213 )
85	X-RAY DIFFRACTION	85	chain 'G' and (resid 214 through 244 )

+
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://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

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
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

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ムービー

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構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)

-ムービー

-構造ビューア

+ビューアのログ

-このページ

-このウェブサイト

-オプション

+データを開く

-基本情報

-構造の表示

-ダウンロードとリンク

-ダウンロード

-検証レポート

-関連構造データ

-リンク

-集合体

-要素

-実験情報

-実験

-試料調製

-データ収集

-解析

+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

-2020年8月12日: 新型コロナ情報

+2020年3月5日: 新型コロナウイルスの構造データ

+2019年1月31日: EMDBのIDの桁数の変更

+2017年7月12日: PDB大規模アップデート

-万見 (Yorodumi)

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)