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万見

- PDB-7jh3: Crystal structure of 4-aminobutyrate aminotransferase PuuE from E... -

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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: 7jh3

タイトル

Crystal structure of 4-aminobutyrate aminotransferase PuuE from Escherichia coli in complex with PLP

要素

4-aminobutyrate aminotransferase PuuE

キーワード

TRANSFERASE / pyridoxalphosphate-dependent aminotransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

機能・相同性

機能・相同性情報

4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / putrescine catabolic process / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / pyridoxal phosphate binding / cytosol
類似検索 - 分子機能

生物種

Escherichia coli (大腸菌)

手法

X線回折 /

分子置換 / 解像度: 2.68 Å

データ登録者

Valleau, D. / Evdokimova, E. / Stogios, P.J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / 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: Crystal structure of 4-aminobutyrate aminotransferase PuuE from Escherichia coli in complex with PLP
著者: Valleau, D.

履歴

登録	2020年7月20日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年8月12日	Provider: repository / タイプ: Initial release
改定 1.1	2023年10月18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
改定 1.2	2023年11月15日	Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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	7jh3.cif.gz	1 MB	表示	PDBx/mmCIF形式
PDB形式	pdb7jh3.ent.gz	784.3 KB	表示	PDB形式
PDBx/mmJSON形式	7jh3.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/jh/7jh3 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/7jh3	HTTPS FTP

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関連構造データ

関連構造データ	6wj8S S: 精密化の開始モデル
類似構造データ	1sf2-d 6rl5-2 6wop-1 1sff-d 1szu-d 6rl5-1 1szk-d 1szs-d 1m0q-1 2eo5-1 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) 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

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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: 4-aminobutyrate aminotransferase PuuE

B: 4-aminobutyrate aminotransferase PuuE

C: 4-aminobutyrate aminotransferase PuuE

D: 4-aminobutyrate aminotransferase PuuE

E: 4-aminobutyrate aminotransferase PuuE

F: 4-aminobutyrate aminotransferase PuuE

ヘテロ分子

270 kDa, 6 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: 4-aminobutyrate aminotransferase PuuE

D: 4-aminobutyrate aminotransferase PuuE

E: 4-aminobutyrate aminotransferase PuuE

F: 4-aminobutyrate aminotransferase PuuE

ヘテロ分子

登録者が定義した集合体
180 kDa, 4 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: 4-aminobutyrate aminotransferase PuuE

C: 4-aminobutyrate aminotransferase PuuE

ヘテロ分子

B: 4-aminobutyrate aminotransferase PuuE

C: 4-aminobutyrate aminotransferase PuuE

ヘテロ分子

登録者が定義した集合体
根拠: In asymmetric unit there are 6 chains, need symmetry for chain B and C to also form second homo-4-mer
180 kDa, 4 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)	198.641, 78.839, 164.976
Angle α, β, γ (deg.)	90.000, 112.823, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	モデル	要素
1	1	B-501- PEG

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要素

#1: タンパク質	4-aminobutyrate aminotransferase PuuE / GABA aminotransferase / GABA-AT / Gamma-amino-N-butyrate transaminase / GABA transaminase / ...GABA aminotransferase / GABA-AT / Gamma-amino-N-butyrate transaminase / GABA transaminase / Glutamate:succinic semialdehyde transaminase 分子量: 45001.000 Da / 分子数: 6 / 由来タイプ: 組換発現由来: (組換発現) Escherichia coli (strain K12) (大腸菌) 株: K12 / 遺伝子: puuE, goaG, b1302, JW1295 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) 参照: UniProt: P50457, 4-aminobutyrate-2-oxoglutarate transaminase
#2: 化合物	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C₄H₁₀O₃
#3: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 465 / 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	N

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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: 2.2 Å³/Da / 溶媒含有率: 44.22 %
結晶化	温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 0.1M di-Na Tartrate, 0.1M Tris pH8.5, 20%PEG3350, 2.2mM PLP, 1%Et.Glycol

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.5418 Å
検出器	タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2017年9月29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: 1.5418 Å / 相対比: 1
反射	解像度: 2.68→25 Å / Num. obs: 67076 / % possible obs: 98.73 % / 冗長度: 3.5 % / B_iso Wilson estimate: 36.6 Å² / R_pim(I) all: 0.051 / Net I/σ(I): 12.1
反射シェル	解像度: 2.68→2.73 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3334 / R_pim(I) all: 0.235

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解析

ソフトウェア

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

精密化

構造決定の手法:

分子置換
開始モデル: 6WJ8

6wj8

解像度: 2.68→24.88 Å / SU ML: 0.2756 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 21.6108
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2

	R_factor	反射数	%反射
R_free	0.2113	1847	2.97 %
R_work	0.1785	60378	-
obs	0.1794	62225	93.79 %

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

B_iso mean: 40.73 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.68→24.88 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	18912	0	14	466	19392

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0044	19308
X-RAY DIFFRACTION	f_angle_d	0.7118	26218
X-RAY DIFFRACTION	f_chiral_restr	0.0487	2946
X-RAY DIFFRACTION	f_plane_restr	0.0051	3474
X-RAY DIFFRACTION	f_dihedral_angle_d	17.8279	6968

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 (%)
2.68-2.75	0.2907	132	0.2465	4263	X-RAY DIFFRACTION	86.86
2.75-2.83	0.299	142	0.247	4375	X-RAY DIFFRACTION	89.16
2.83-2.92	0.2976	131	0.2463	4447	X-RAY DIFFRACTION	90.01
2.92-3.03	0.256	142	0.2309	4521	X-RAY DIFFRACTION	91.52
3.03-3.15	0.2511	143	0.228	4594	X-RAY DIFFRACTION	93.12
3.15-3.29	0.2649	145	0.2072	4570	X-RAY DIFFRACTION	93.53
3.29-3.47	0.24	143	0.2034	4596	X-RAY DIFFRACTION	93.69
3.47-3.68	0.2236	142	0.1864	4748	X-RAY DIFFRACTION	95.43
3.68-3.97	0.2024	142	0.1661	4730	X-RAY DIFFRACTION	95.57
3.97-4.36	0.1836	139	0.1479	4771	X-RAY DIFFRACTION	96.27
4.36-4.99	0.1688	150	0.1354	4840	X-RAY DIFFRACTION	97.8
4.99-6.27	0.1651	144	0.1529	4875	X-RAY DIFFRACTION	97.19
6.27-24.88	0.1575	152	0.1432	5048	X-RAY DIFFRACTION	98.8

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	1.60760276269	-1.90557807878	-0.215503604938	5.41475755225	-1.53493794743	3.02812348476	0.0191412574698	-0.441765966316	0.371052678764	0.491301628088	0.0500001099484	-0.0966106344504	-0.129165781748	-0.425306648196	-0.0690291073756	0.4711465263	-0.0110354148643	-0.0464478988374	0.585952489454	-0.0342663170423	0.342621898647	92.1534313428	30.9421323734	80.8722742109
2	2.97406400955	-0.0945089731775	0.556025835686	2.3105574954	1.44112776274	1.12448996109	-0.157151933766	-0.293435282094	0.0147637667366	0.102679593407	0.14115828845	0.159623238467	0.154216734759	-0.178458510218	0.0288585241314	0.316841911334	0.0426337573047	0.0218751666699	0.360295215162	0.0315655905057	0.276556464255	76.2193066736	35.8886422106	70.8097739437
3	7.09898610382	5.15952595929	5.14420524691	4.63512880789	4.62107883156	4.62920211062	0.277380273583	-0.815899090353	0.499047086744	0.218137620663	-0.524199088142	0.870238497042	0.55087228709	-1.43308335296	0.177764966589	0.425614925672	0.0380466579492	0.0480004126341	0.572843452462	0.124931634392	0.525924394985	70.913466209	19.2006311729	57.6007540166
4	0.907104109088	-2.80850915384	0.996270512149	8.10584884838	-2.06240557441	3.29514755256	0.0736774684764	0.135368980218	0.0868064065164	-0.527892578936	-0.127224681727	-0.180192656785	0.133762248184	-0.0981604071505	0.0591367334524	0.241599732436	-0.0630951392645	-0.0229105738991	0.261584610848	0.0602884905645	0.220698509572	80.6850251308	26.2750059305	45.6356837051
5	2.09087051414	1.45678445521	0.00595464730917	1.01804759825	-0.515391283059	2.10352779024	0.0413389081383	-0.0275007430346	-0.0374384811364	0.109292834945	0.00411361148289	0.0495090424795	-0.205166395519	0.157181477054	-0.0369745717917	0.324703264625	0.0295588609758	-0.0345228214016	0.220520793015	0.0331981527878	0.288987698997	100.099789985	37.2272159212	52.2528321872
6	8.24324093855	4.95382416879	1.68382242809	3.25649889678	2.41389682074	7.18208618074	-0.261592187677	-0.641257357808	0.449701381467	0.0846468787503	-0.727479700491	0.677238532418	0.651364260644	0.794099858846	0.676630842102	0.802144425224	0.0603916644753	0.118100285876	0.477525021376	0.042884608177	0.38282051791	96.6007746818	58.2272384319	57.6823025125
7	7.47636163371	-1.83708521495	-4.30403792894	3.85020334183	1.7873503234	3.47841546542	0.160097800344	-0.0261483873938	0.498059640226	-0.181860068795	0.202311904316	0.201259315784	-0.381529217858	0.190406841975	-0.303197734419	0.316076078888	0.00309159868859	-0.0370694118699	0.256784822428	0.0677150763359	0.245489064254	100.641905173	51.0789452811	48.2353705899
8	1.31870323246	0.456614163882	-0.0313394686286	0.756404552609	-0.17351700856	0.774980688546	0.0321166270088	0.108732188389	0.0859268110899	-0.00447837626744	-0.00735018711694	0.0247741007395	-0.10164321175	-0.010529125942	-0.0270197383575	0.28666710442	0.0384332505325	-0.0135083544825	0.272527199486	0.0375507483052	0.224223612558	87.510245406	38.2946312142	47.6008110379
9	6.07333866066	0.545508655235	5.01990178869	9.88698480218	-1.03677564452	8.01519144826	0.231726249822	0.141656091629	-0.475059435425	-0.461353631881	-0.0218325813062	1.63007138142	0.967091082212	-1.03328426864	-0.23131036084	0.436654058242	0.0465225011422	0.043795857271	0.644478864953	0.106168163874	0.495227978569	68.3381273562	40.0790396522	53.8893641315
10	9.66533655559	0.794185328799	-3.43012684657	7.71394438685	2.43573133742	6.82177431759	0.162911065903	0.728247661633	1.08460066275	-0.493715786022	-0.462688521871	0.764399123158	-0.619222831239	-0.0289714191124	0.260484245277	0.407610522016	0.038528743188	0.0348923054251	0.346188856216	0.0554828094069	0.62353867622	72.2950484438	48.8784090886	56.4253458252
11	4.81400787007	0.666702857513	0.750612196928	3.35367547723	1.72456079987	4.50714163038	-0.0601728272247	-0.117620135609	0.604918008276	0.165962831757	0.128351646695	-0.130178760057	-0.253450845314	0.591031586175	-0.0789281455713	0.349995450455	0.00292532543427	0.0330867860507	0.302955017003	-0.0239333574772	0.397995843487	85.923811045	54.9622563812	69.9111072999
12	8.46391462335	1.11765152655	0.534947466342	5.4614723931	-3.28369181808	5.89818783191	0.278528335758	-0.555047677031	1.30374349681	0.763351282424	-0.28824262549	0.249734897619	-0.429935456084	-0.681382259745	0.113408510969	0.418396872754	0.0612064915033	0.12637757578	0.330580983382	-0.0863078833863	0.501373817669	75.3712318693	53.8725551761	74.66648412
13	4.89900695999	4.95757118312	4.13716160869	4.98101473469	4.24419757291	4.09840454742	-0.056389771474	0.418256881411	-0.40471010062	-0.344437452273	0.0457793090427	-0.1574798685	-0.0668143727818	0.272424286881	0.01589356513	0.336126908914	0.0532507631539	-0.0346941557834	0.496662999783	0.0177635329957	0.30131674155	123.052669719	39.4129477713	-29.5334518015
14	6.9036066022	1.8164129493	2.52775044305	5.28054790002	5.40100927268	5.73001566889	-0.010291338448	1.01173872791	0.263330300113	-0.618179989435	-0.224369585016	-0.292627370993	-0.641590740644	0.370624734496	0.370482694864	0.391637557328	-0.0973216163938	-0.0329962635114	0.622385539559	0.1329878155	0.391820932213	136.754312888	47.9959634928	-25.651169423
15	1.53185158853	0.0945914832784	-0.757848574981	1.47549838385	0.14886200014	0.59219166195	-0.0038564149322	0.496881144593	0.0838337069646	-0.138207499589	0.0532495670866	-0.233686463227	0.0270250581804	0.0185534203692	-0.0629839649624	0.333603136731	-0.038844469163	-0.0201336338071	0.419486144211	0.0402028434655	0.302713582284	136.512119606	46.5732428469	-13.4389733293
16	0.0794898515597	0.368598318088	0.0754712770238	2.85989547389	2.08178316313	4.68314840301	0.141001660741	-0.0265621844218	-0.058462574702	-0.108382326365	-0.0747893795131	-0.296886749242	0.0317691567946	0.424575284961	-0.0741291632617	0.245356807823	0.0211232703954	-0.0294072999994	0.354983274055	-0.0411993080617	0.322642620866	135.878683882	33.9130802594	3.26997425204
17	1.82622741484	-0.0221682510634	0.487342829476	0.600463709389	0.351510502623	0.290166210956	0.000189253317723	-0.0128881412705	0.0571637771695	-0.0356013286167	0.0305139096129	-0.0515191681069	-0.135572975953	-0.0191361474689	-0.0264188174531	0.309625757261	-0.0189343165571	-0.00383952280211	0.200490282893	-0.00555229797387	0.260153435624	112.365790196	41.3419196636	-0.859409835608
18	2.47727419503	-0.182966895907	0.363918730567	3.53196494569	-3.62441144434	5.20542642974	1.02314638535	0.0836787931755	0.300833667549	-0.949605387153	-1.14011398368	-0.185976686151	-2.69238943353	0.710301516052	0.0880810653055	0.93512517702	0.0325143605332	-0.0878247649595	0.475655622577	0.0341238312218	0.549480837707	108.512580939	64.2230693187	-5.66231984524
19	6.95456563858	4.67719063675	-3.05706525434	3.82481776832	-1.92327428933	2.19478048303	0.452123222614	-0.136590629334	1.01134342838	0.345077920816	0.108763447244	0.726689232473	-0.64806540751	-0.117395333084	-0.309618966928	0.338488494323	0.0149949366273	0.0601019122097	0.247233641668	-0.0640285445558	0.414675470598	101.254053025	52.9098737292	7.90188861075
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56	3.50981846137	2.39038906556	-0.977616906764	5.59042752951	-1.7991627079	1.03623964052	-0.187284391564	-0.12970098493	0.252924855897	0.244598773333	0.288022773375	0.163668689711	-0.167342985964	-0.292492524976	-0.0659682084135	0.388755628889	0.012620838739	-0.0353175303276	0.253864343333	-0.0697359682473	0.20579364095	118.042693422	54.9744699219	56.5285308382
57	0.843769421671	-0.180705993876	-0.395545735043	0.684760531089	0.238202393704	1.34147143045	0.0246705013056	-0.0376073377327	0.10038855018	0.171805816711	-0.0416626084413	-0.0374786187779	-0.0287111331907	-0.0685180793174	0.0137767580316	0.32698354567	-0.0272428987626	-0.0565178136078	0.26870089807	-0.0502731250147	0.289552691509	137.104574609	51.4973592801	55.647879196
58	5.24690282003	-5.4966391245	2.48982825131	6.07244533379	-4.10045641302	8.50882481208	-0.32179559024	-0.490948750096	1.27060221135	0.70000458352	-0.24884533651	-1.65193811362	-0.518937577126	0.590888578692	0.431666681144	0.433829763796	-0.105608308213	0.000216392859002	0.363847018342	-0.104900241976	0.445621130277	143.660739418	68.4375927208	49.1956486277
59	4.93334843634	-2.90075621403	0.646692610831	2.1686825003	-0.879157045303	2.86438535355	0.07040996389	0.153134013414	-0.0112443333552	-0.0810929669788	0.0531952111861	0.166377187104	-0.12360741129	-0.261868883639	-0.106594768307	0.39541165471	-0.0134776658331	0.00869052082567	0.301130511162	-0.0191541022202	0.38457026967	129.903456265	68.8633932746	35.9875393217
60	7.78561530028	-4.66115588039	2.78423877585	3.40290992744	-1.22580855829	3.27846010318	0.486360443042	1.00219840071	1.93528564523	-1.11970950963	-1.06481255064	-0.68743091814	-0.454062152507	-0.299564540429	0.566737383153	0.609646763289	0.0311303234325	0.0571858381297	0.447997253538	-0.0102990345367	0.569517377096	132.2245599	74.7009676254	28.4044915023
61	6.49303230188	-3.01173885923	-5.25181189618	4.55895948234	-1.7573382291	9.87005656209	0.528900160945	1.31276285357	-1.39934226818	-0.483125439175	-0.237045289478	0.934745808046	0.492738733532	-1.05722687524	-0.460559448807	0.6277660562	-0.0443245221011	-0.199837346615	0.719260280242	-0.0241308597691	0.438477943198	76.1976620537	19.863476123	35.5770012546
62	4.16387376477	5.27219810642	-4.26535701324	7.88197334722	-6.24277294933	5.88564849584	0.089578828749	0.354381240643	0.159587991367	-0.00939286755074	0.107181821911	0.304815141717	-0.145532632209	-0.27452740468	-0.158051042647	0.33018544997	-0.0366031986624	-0.0102370441754	0.349032297658	-0.0340110155383	0.301594239792	81.7682291571	16.3662758921	44.0777199553
63	5.43829504612	-4.79827655146	-1.72259060178	4.26952365414	1.80411358361	3.14200750026	0.311785707946	1.32593267714	-0.369119229628	0.928360228292	-0.495001976134	0.335003427736	0.374380958884	-0.595545619062	0.118584707058	0.419163848398	-0.220590046382	-0.0146587657291	0.545574126346	-0.0682933801576	0.473135797589	72.4635188875	8.79998810506	44.2602316766
64	0.597539606697	0.0572553772728	-1.01909480317	0.749576207254	0.0732988860712	1.90714750082	0.0126811675937	0.0388100928972	-0.175542483775	-0.108670827055	-0.134658665495	0.0331149755568	-0.0253550346979	-0.207372360524	0.193132298273	0.361794854083	-0.0181882054595	-0.0189559297144	0.285766036221	0.0357424174917	0.311526777584	81.3705895122	10.1073624016	58.7199102066
65	4.23953154196	5.09963713958	5.04203296979	7.65015836233	4.83002206188	8.6814219727	0.0897726096259	-0.180559714492	-0.530499675703	0.27684656027	0.195910350937	0.00524395506799	-0.051176175342	-0.180028263207	-0.254006120066	0.318270330663	0.0453274261251	0.0320102142174	0.315992490438	0.0712781983771	0.428618386885	80.8895498346	28.9865528416	71.3745770978
66	2.39007236995	0.0647063089123	-1.70663093528	0.570089870382	-0.448642793556	1.39687863665	-0.0297146266801	-0.297233781602	-0.0775083049795	0.105444163347	0.0305957165645	0.034003422967	0.0929466720196	0.110390506999	0.000343624364701	0.339709732011	0.0223799223634	-0.0454893764053	0.298172133488	-0.00258493596609	0.201661187057	101.463615759	21.9370546931	68.0046445574
67	4.18123311924	-1.88634578156	0.835861491884	1.2707992866	-0.880410953314	3.66517162043	-0.00815244138272	-0.0082610552632	-0.208907692573	-0.120162654858	0.115620632647	0.150630936567	0.161949475215	-0.073008373975	-0.0799202464086	0.292429417412	-0.0118556290558	-0.00837990739228	0.219505602241	0.0164713700459	0.264298742393	106.83675733	20.3412134672	49.8970144284
68	5.26095370416	3.28544367893	0.167022665279	5.46137709666	0.811267163262	0.423200073682	-0.254548923798	0.0839801593908	-0.296320767336	-0.189885806885	0.244673071461	-0.0435770507731	0.157301337707	0.243377452444	-0.00674712377973	0.342561170695	0.0426607875362	-0.0191952814211	0.246236148832	0.0710284042813	0.204699115247	114.67019985	11.7931473311	57.225367034
69	1.6057792207	-0.356999702974	0.568806663629	0.57967589202	-0.0548094865227	0.404221849218	-0.0251350071815	-0.0582320789498	-0.177584422985	0.0235698553383	0.0175136159648	-0.0310718194947	0.103011222927	0.096876272825	0.00571933847247	0.398498040701	0.0240467631034	-0.00562656550079	0.275791714532	0.0793152001721	0.251888497897	99.3724414568	16.5619095262	67.2542838928
70	9.04746772408	-1.83791658141	-5.16831004826	9.47812198618	4.57769516996	4.45980932155	-0.126948230823	-1.32475942473	-0.933153700192	0.42460886598	-0.000843304318871	0.218552482548	0.559159524603	0.748204813921	0.180102457786	0.479392537655	-0.00377314550105	0.0127935562325	0.375623026442	0.129927339999	0.455018770548	86.4810522365	2.24324137414	70.3051328993
71	1.13678724841	-0.380715351019	-0.308145366391	4.06910074025	0.324403334734	2.68138028834	-0.0823203006432	0.281549001865	-0.398297323719	-0.304898748586	0.186043821909	0.0480316737245	0.382929184104	-0.162701532418	-0.134215385804	0.420790708898	0.0253627944284	-0.016205379179	0.325489589292	0.0127538463828	0.489256933034	97.2867063439	-4.12886534588	47.3672881019
72	6.58049996667	0.434181619631	-2.98884564415	5.59010564559	1.40757233168	6.45967186709	-0.0649388526087	0.482199719165	-0.291315735156	-0.591971578637	-0.00894579909111	0.151923493849	-0.0163522532966	-0.22618923651	0.0627854372197	0.360752599586	0.0466636098653	-0.0539813653227	0.266888217173	-0.0267451951443	0.353314354237	88.3262209345	-0.135638667781	47.3221155295

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:23)
2	X-RAY DIFFRACTION	2	(chain A and resid 24:65)
3	X-RAY DIFFRACTION	3	(chain A and resid 66:71)
4	X-RAY DIFFRACTION	4	(chain A and resid 72:100)
5	X-RAY DIFFRACTION	5	(chain A and resid 101:169)
6	X-RAY DIFFRACTION	6	(chain A and resid 170:175)
7	X-RAY DIFFRACTION	7	(chain A and resid 176:221)
8	X-RAY DIFFRACTION	8	(chain A and resid 222:311)
9	X-RAY DIFFRACTION	9	(chain A and resid 312:318)
10	X-RAY DIFFRACTION	10	(chain A and resid 319:324)
11	X-RAY DIFFRACTION	11	(chain A and resid 325:403)
12	X-RAY DIFFRACTION	12	(chain A and resid 404:421)
13	X-RAY DIFFRACTION	13	(chain B and resid 2:27)
14	X-RAY DIFFRACTION	14	(chain B and resid 28:41)
15	X-RAY DIFFRACTION	15	(chain B and resid 42:66)
16	X-RAY DIFFRACTION	16	(chain B and resid 67:100)
17	X-RAY DIFFRACTION	17	(chain B and resid 101:171)
18	X-RAY DIFFRACTION	18	(chain B and resid 172:177)
19	X-RAY DIFFRACTION	19	(chain B and resid 178:197)
20	X-RAY DIFFRACTION	20	(chain B and resid 198:219)
21	X-RAY DIFFRACTION	21	(chain B and resid 220:277)
22	X-RAY DIFFRACTION	22	(chain B and resid 278:341)
23	X-RAY DIFFRACTION	23	(chain B and resid 342:397)
24	X-RAY DIFFRACTION	24	(chain B and resid 398:421)
25	X-RAY DIFFRACTION	25	(chain C and resid 2:22)
26	X-RAY DIFFRACTION	26	(chain C and resid 23:38)
27	X-RAY DIFFRACTION	27	(chain C and resid 39:65)
28	X-RAY DIFFRACTION	28	(chain C and resid 66:102)
29	X-RAY DIFFRACTION	29	(chain C and resid 103:173)
30	X-RAY DIFFRACTION	30	(chain C and resid 174:219)
31	X-RAY DIFFRACTION	31	(chain C and resid 220:311)
32	X-RAY DIFFRACTION	32	(chain C and resid 312:322)
33	X-RAY DIFFRACTION	33	(chain C and resid 323:340)
34	X-RAY DIFFRACTION	34	(chain C and resid 341:369)
35	X-RAY DIFFRACTION	35	(chain C and resid 370:376)
36	X-RAY DIFFRACTION	36	(chain C and resid 377:421)
37	X-RAY DIFFRACTION	37	(chain D and resid 2:27)
38	X-RAY DIFFRACTION	38	(chain D and resid 28:44)
39	X-RAY DIFFRACTION	39	(chain D and resid 45:99)
40	X-RAY DIFFRACTION	40	(chain D and resid 100:136)
41	X-RAY DIFFRACTION	41	(chain D and resid 137:171)
42	X-RAY DIFFRACTION	42	(chain D and resid 172:177)
43	X-RAY DIFFRACTION	43	(chain D and resid 178:198)
44	X-RAY DIFFRACTION	44	(chain D and resid 199:320)
45	X-RAY DIFFRACTION	45	(chain D and resid 321:339)
46	X-RAY DIFFRACTION	46	(chain D and resid 340:374)
47	X-RAY DIFFRACTION	47	(chain D and resid 375:408)
48	X-RAY DIFFRACTION	48	(chain D and resid 409:421)
49	X-RAY DIFFRACTION	49	(chain E and resid 1:22)
50	X-RAY DIFFRACTION	50	(chain E and resid 23:38)
51	X-RAY DIFFRACTION	51	(chain E and resid 39:65)
52	X-RAY DIFFRACTION	52	(chain E and resid 66:83)
53	X-RAY DIFFRACTION	53	(chain E and resid 84:138)
54	X-RAY DIFFRACTION	54	(chain E and resid 139:169)
55	X-RAY DIFFRACTION	55	(chain E and resid 170:175)
56	X-RAY DIFFRACTION	56	(chain E and resid 176:220)
57	X-RAY DIFFRACTION	57	(chain E and resid 221:318)
58	X-RAY DIFFRACTION	58	(chain E and resid 319:324)
59	X-RAY DIFFRACTION	59	(chain E and resid 325:412)
60	X-RAY DIFFRACTION	60	(chain E and resid 413:421)
61	X-RAY DIFFRACTION	61	(chain F and resid 2:9)
62	X-RAY DIFFRACTION	62	(chain F and resid 10:34)
63	X-RAY DIFFRACTION	63	(chain F and resid 35:41)
64	X-RAY DIFFRACTION	64	(chain F and resid 42:65)
65	X-RAY DIFFRACTION	65	(chain F and resid 66:83)
66	X-RAY DIFFRACTION	66	(chain F and resid 84:136)
67	X-RAY DIFFRACTION	67	(chain F and resid 137:173)
68	X-RAY DIFFRACTION	68	(chain F and resid 174:220)
69	X-RAY DIFFRACTION	69	(chain F and resid 221:313)
70	X-RAY DIFFRACTION	70	(chain F and resid 314:321)
71	X-RAY DIFFRACTION	71	(chain F and resid 322:374)
72	X-RAY DIFFRACTION	72	(chain F and resid 375:421)

+
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://pdbjlc1.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

-
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)

-
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)