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万見

- PDB-6v96: Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72E -

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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: 6v96

タイトル

Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72E

要素

Glucose-1-phosphate adenylyltransferase

キーワード

TRANSFERASE / Allosteric regulation / Fructose 6-phosphate / Glycogen synthesis / enzyme structure

機能・相同性

機能・相同性情報

glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / ATP binding
類似検索 - 分子機能

生物種

Agrobacterium fabrum (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: 1.8 Å

データ登録者

Zheng, Y. / Hussien, R. / Alghamdi, M.A. / Ballicora, M.A. / Liu, D.

資金援助

米国, 1件

引用

ジャーナル: Protein Sci. / 年: 2022
タイトル: Site-directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase.
著者: Alghamdi, M.A. / Hussien, R.A. / Zheng, Y. / Patel, H.P. / Asencion Diez, M.D. / A Iglesias, A. / Liu, D. / Ballicora, M.A.

履歴

登録	2019年12月13日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2020年12月16日	Provider: repository / タイプ: Initial release
改定 1.1	2022年7月6日	Group: Advisory / Database references カテゴリ: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.2	2023年10月11日	Group: Data collection / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア	分子: MolmilJmol/JSmol

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ダウンロードとリンク

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ダウンロード

PDBx/mmCIF形式	6v96.cif.gz	4 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6v96.ent.gz	2.8 MB	表示	PDB形式
PDBx/mmJSON形式	6v96.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

文書・要旨	6v96_validation.pdf.gz	323.9 KB	表示	wwPDB検証レポート
文書・詳細版	6v96_full_validation.pdf.gz	342.7 KB	表示
XML形式データ	6v96_validation.xml.gz	6.7 KB	表示
CIF形式データ	6v96_validation.cif.gz	121 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/v9/6v96 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v96	HTTPS FTP

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関連構造データ

関連構造データ	6v99C 6v9aC 5w6jS S: 精密化の開始モデル C: 同じ文献を引用 (文献)
類似構造データ	6v9a-2 6v99-5 6v99-1 6v9a-4 6v9a-1 5w6j-4 5w5r-4 6v99-3 5w5t-2 6v9a-3 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

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リンク

PDBのページ	PDBj / wwPDB / NCBI
「今月の分子」の関連する項目	#156 - 2012年12月 ABO式血液型糖転移酵素 (ABO Blood Type Glycosyltransferases) 類似性 (1) #254 - 2021年2月セルロース合成酵素 (Cellulose Synthase) 類似性 (1) #165 - 2013年9月人工設計されたタンパク質製の籠 (Designed Protein Cages) 類似性 (1) #39 - 2003年3月 lac転写抑制因子 (lac Repressor) 類似性 (1) #49 - 2004年1月炭酸脱水酵素 (Carbonic Anhydrase) 類似性 (1)

PDBのページ

PDBj /

wwPDB /

NCBI

「今月の分子」の関連する項目

#156 - 2012年12月
ABO式血液型糖転移酵素 (ABO Blood Type Glycosyltransferases)
類似性 (1)
#254 - 2021年2月
セルロース合成酵素 (Cellulose Synthase)
類似性 (1)
#165 - 2013年9月
人工設計されたタンパク質製の籠 (Designed Protein Cages)
類似性 (1)
#39 - 2003年3月
lac転写抑制因子 (lac Repressor)
類似性 (1)
#49 - 2004年1月
炭酸脱水酵素 (Carbonic Anhydrase)
類似性 (1)

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集合体

登録構造単位

H: Glucose-1-phosphate adenylyltransferase

A: Glucose-1-phosphate adenylyltransferase

B: Glucose-1-phosphate adenylyltransferase

C: Glucose-1-phosphate adenylyltransferase

D: Glucose-1-phosphate adenylyltransferase

E: Glucose-1-phosphate adenylyltransferase

F: Glucose-1-phosphate adenylyltransferase

G: Glucose-1-phosphate adenylyltransferase

I: Glucose-1-phosphate adenylyltransferase

J: Glucose-1-phosphate adenylyltransferase

K: Glucose-1-phosphate adenylyltransferase

L: Glucose-1-phosphate adenylyltransferase

M: Glucose-1-phosphate adenylyltransferase

N: Glucose-1-phosphate adenylyltransferase

O: Glucose-1-phosphate adenylyltransferase

P: Glucose-1-phosphate adenylyltransferase

Q: Glucose-1-phosphate adenylyltransferase

R: Glucose-1-phosphate adenylyltransferase

V: Glucose-1-phosphate adenylyltransferase

T: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

992 kDa, 20 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: Glucose-1-phosphate adenylyltransferase

G: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

O: Glucose-1-phosphate adenylyltransferase

P: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
根拠: gel filtration
198 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)

A: Glucose-1-phosphate adenylyltransferase

B: Glucose-1-phosphate adenylyltransferase

C: Glucose-1-phosphate adenylyltransferase

D: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
198 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)

E: Glucose-1-phosphate adenylyltransferase

F: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

Q: Glucose-1-phosphate adenylyltransferase

R: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
198 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)

I: Glucose-1-phosphate adenylyltransferase

J: Glucose-1-phosphate adenylyltransferase

M: Glucose-1-phosphate adenylyltransferase

N: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
198 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)

K: Glucose-1-phosphate adenylyltransferase

L: Glucose-1-phosphate adenylyltransferase

V: Glucose-1-phosphate adenylyltransferase

T: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
198 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)	93.607, 141.187, 229.427
Angle α, β, γ (deg.)	107.926, 101.725, 89.970
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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要素

#1: タンパク質	Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase / ADPGlc PPase / ADP-glucose synthase 分子量: 49314.543 Da / 分子数: 20 / 変異: S72E / 由来タイプ: 組換発現由来: (組換発現) Agrobacterium fabrum (strain C58 / ATCC 33970) (バクテリア) 株: C58 / ATCC 33970 / 遺伝子: glgC, Atu4076, AGR_L_1560 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) 参照: UniProt: Q8U8L5, glucose-1-phosphate adenylyltransferase
#2: 化合物	ChemComp-CIT / CITRIC ACID / クエン酸分子量: 192.124 Da / 分子数: 20 / 由来タイプ: 合成 / 式: C₆H₈O₇
#3: 化合物	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル分子量: 92.094 Da / 分子数: 22 / 由来タイプ: 合成 / 式: C₃H₈O₃
#4: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 7860 / 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: 2.98 Å³/Da / 溶媒含有率: 58.67 %
結晶化	温度: 297 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: Sodium citrate, imidazole

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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: 21-ID-F / 波長: 0.978 Å
検出器	タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2018年2月6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: 0.978 Å / 相対比: 1
反射	解像度: 1.79→37.4 Å / Num. obs: 776640 / % possible obs: 82 % / 冗長度: 1.5 % / B_iso Wilson estimate: 32.4 Å² / R_pim(I) all: 0.042 / R_rim(I) all: 0.06 / Net I/σ(I): 1
反射シェル	解像度: 1.79→1.83 Å / Num. unique obs: 41416 / CC_1/2: 0.604

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.11.1_2575	精密化
HKL-2000		データ削減
SCALEPACK		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: 5W6J

5w6j

解像度: 1.8→37.39 Å / SU ML: 0.199 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 27.26

	R_factor	反射数	%反射
R_free	0.2276	38499	4.96 %
R_work	0.1933	-	-
obs	0.195	776639	76.7 %

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: 32.4 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.8→37.39 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	64902	0	392	7860	73154

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0109214215798	67745
X-RAY DIFFRACTION	f_angle_d	1.08852349092	92169
X-RAY DIFFRACTION	f_chiral_restr	0.0691317740712	10018
X-RAY DIFFRACTION	f_plane_restr	0.00740218075811	12152
X-RAY DIFFRACTION	f_dihedral_angle_d	8.16580110076	55227

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 (%)
1.7996-1.82	0.3366	409	0.3058	8822	X-RAY DIFFRACTION	27.4283167434
1.82-1.8414	0.359555289101	557	0.302482518392	11450	X-RAY DIFFRACTION	35.4691007917
1.8414-1.8639	0.33876484012	746	0.294920815268	14403	X-RAY DIFFRACTION	44.8420803363
1.8639-1.8875	0.344935677827	1005	0.286221124807	18675	X-RAY DIFFRACTION	58.4531305691
1.8875-1.9123	0.314105236742	1204	0.265892469139	22126	X-RAY DIFFRACTION	68.974692526
1.9123-1.9385	0.291692753537	1124	0.261610051344	24147	X-RAY DIFFRACTION	74.9614380636
1.9385-1.9662	0.288039647571	1255	0.249870369078	24874	X-RAY DIFFRACTION	77.5663480378
1.9662-1.9956	0.278735834336	1280	0.242762237846	26237	X-RAY DIFFRACTION	81.1351909185
1.9956-2.0267	0.274528572867	1360	0.226838889296	26618	X-RAY DIFFRACTION	83.0035304239
2.0267-2.06	0.272551625434	1379	0.226643834802	26460	X-RAY DIFFRACTION	82.9405630865
2.06-2.0955	0.257987094432	1368	0.22103123653	26578	X-RAY DIFFRACTION	82.441441973
2.0955-2.1336	0.266628125849	1350	0.224840853019	26325	X-RAY DIFFRACTION	82.1143518381
2.1336-2.1746	0.261750144702	1413	0.218542217529	26282	X-RAY DIFFRACTION	81.5926700645
2.1746-2.219	0.255208211508	1336	0.204718624284	25950	X-RAY DIFFRACTION	81.2397653854
2.219-2.2672	0.252157021787	1286	0.199983560946	25907	X-RAY DIFFRACTION	80.4288671991
2.2672-2.32	0.247804625279	1397	0.199679842676	25593	X-RAY DIFFRACTION	79.6517633171
2.32-2.378	0.24786784825	1333	0.196941767917	25087	X-RAY DIFFRACTION	78.8045099326
2.378-2.4423	0.243807997816	1306	0.195983177942	25235	X-RAY DIFFRACTION	78.3035845995
2.4423-2.5141	0.230858774108	1271	0.202008472746	24916	X-RAY DIFFRACTION	77.5313832307
2.5141-2.5953	0.243766035806	1370	0.200775587589	24477	X-RAY DIFFRACTION	76.5406141728
2.5953-2.688	0.235168813944	1259	0.199943633303	24376	X-RAY DIFFRACTION	76.1586452763
2.688-2.7956	0.226204299281	1360	0.196763204782	24454	X-RAY DIFFRACTION	76.3660030175
2.7956-2.9228	0.222617211719	1235	0.193274145312	24718	X-RAY DIFFRACTION	76.6683406694
2.9228-3.0768	0.22660468088	1413	0.187299170933	25341	X-RAY DIFFRACTION	79.4264339152
3.0768-3.2695	0.205856136274	1460	0.187389806759	27150	X-RAY DIFFRACTION	84.7377306519
3.2695-3.5217	0.20965581855	1488	0.175462906915	29314	X-RAY DIFFRACTION	91.3653486786
3.5217-3.8758	0.193859242464	1831	0.155624708929	30693	X-RAY DIFFRACTION	96.3788300836
3.8758-4.4358	0.168115165549	1608	0.145957168571	31531	X-RAY DIFFRACTION	97.9748107852
4.4358-5.5857	0.186646760869	1634	0.161230036881	31357	X-RAY DIFFRACTION	97.8380782918
5.5857-37.3	0.236534770139	1462	0.208507494887	29045	X-RAY DIFFRACTION	90.3215300805

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	1.90146520437	0.344189337292	0.0478175954377	2.27253596721	0.224933930231	1.26585723025	-0.0776951809027	0.0580329378843	-0.0229199773981	-0.298661380526	0.106592820674	-0.0455258165193	0.00562941630907	-0.0472528101112	-0.0411328700132	0.166483263932	0.0231100001557	0.0302105862984	0.140542841734	-0.0126229929533	0.10265756249	26.8985169168	22.3430108204	16.3543636441
2	3.56370973933	0.757666810836	0.213769830391	3.1938684548	1.2955313575	4.40042213507	-0.00306216780095	0.141585310156	-0.0949725979088	-0.377626259246	-0.0823140525042	0.140877334311	0.05888857389	-0.153489826004	0.0375005980637	0.163218437476	0.0588302218226	-0.00880592342464	0.150315221482	-0.00359469249635	0.132216400413	19.9675474886	29.9615394711	17.8056727848
3	1.55612660433	0.83784409154	-0.537644643362	3.61782550911	0.423938891163	2.87925254458	-0.0767669620973	0.383471230582	0.227754073315	-0.732328974794	0.0960869281783	0.291421755431	-0.575149766834	-0.280785100681	-0.129417225076	0.327801187406	0.0237499091721	0.0265144921295	0.225114959933	0.00738668302676	0.178048965038	29.9438389627	32.4041951434	9.10780200934
4	0.00994063512933	-0.0351677764175	-0.0472422408267	0.225165626634	0.292054155726	0.377844047014	0.0432707068539	0.15832899131	-0.0193383523651	-0.419119547092	0.0569253026076	-0.418334233152	-0.130710341288	0.253428378316	-0.10342609441	0.332223322199	-0.0260763052143	0.258200778146	0.286848320933	-0.0921823670639	0.433813150556	45.5906471325	23.6128210632	8.48251100213
5	1.17755965231	0.195619698858	-0.0805870913693	1.51743168281	0.199483132178	1.10470468812	0.0401999674157	0.0201546385312	-0.0637637329947	-0.231778466204	0.0276732673551	0.0121114751173	0.133419945756	-0.0344234158272	-0.0703566755484	0.177356808918	0.00121211619345	-0.0376819124596	0.152311591889	0.00438709356258	0.132008217271	18.169832833	3.05780737883	21.8422706859
6	2.19799131259	-1.03404213484	-1.14170481834	1.17825369319	0.768450775135	2.28866255467	0.0632055019701	0.429271583555	-0.213833865665	-0.254608320675	-0.0931622707696	0.136411644317	0.124919281453	-0.277420629287	0.0829296261778	0.459999237811	-0.00898392000714	-0.0907301581348	0.220696633702	-0.048219466884	0.108651601491	13.8490498151	-1.25958822901	3.65494084531
7	2.02872287887	0.155892604757	-0.0750352560498	1.87918835764	-0.524369337852	2.22940232263	0.0610726223073	0.0132086820265	-0.0775276855159	-0.366448623622	0.0723332296429	0.0929855720149	0.0201096924795	0.0231488453989	-0.138036678578	0.215599636807	0.0266617010059	-0.0356975209603	0.12912726042	-0.0103319568017	0.110190220619	-44.1963118459	-28.258156058	59.3354111198
8	4.18495451325	0.323295076099	0.248752959774	2.29022132185	-0.993168479342	4.14612123893	0.0492813420751	0.15830434006	0.0999489275293	-0.562778652909	-0.0270007836555	-0.10909903684	0.00814854498748	0.230135517946	-0.0420407456516	0.216329990636	0.0350701469726	0.0229503353512	0.166046476333	0.00213522002831	0.142383061516	-37.1811136467	-35.9371433826	60.5590940849
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119	3.20070892061	-0.983445209807	-0.127202771623	2.23452591261	1.13183052925	4.14895867784	0.0912894040747	-0.174640477697	0.0676575051697	0.485000442297	-0.0359688380798	0.127040712799	0.102885592118	-0.0692265562764	-0.0964994205456	0.264386263944	-0.0931718522668	0.0171251006973	0.153611902275	0.000660846128763	0.147573826879	-26.4851548161	-36.6206197637	1.17341495559
120	1.64840248503	-0.544216018591	2.16551077335	6.29391280973	3.44349333034	5.67394746694	-0.0495952761671	-0.385389236246	-0.0335798491147	0.952165336882	-0.109790988841	0.322341722529	0.390879606607	-0.690404115311	0.122863673824	0.813279345938	-0.0791561668	-0.065849040292	0.273780686124	0.0147653290853	0.220073681995	-19.9983548517	-43.7234533051	14.2269787687
121	0.125637118083	-0.0825618004552	0.0763445681365	0.073931773458	0.0202880751217	0.248080151946	-0.00229304171469	-0.0469368387132	-0.0415435938456	0.335013608625	0.0716126871944	-0.41009202946	0.156034033631	0.182458473797	-0.373141664937	0.397457819807	0.0244647974381	-0.386520473796	0.2591626768	-0.149150852596	0.51257085017	-2.35010345692	-30.9986981939	10.0558375089
122	1.39939236325	-0.152713295396	0.305054755154	1.55520427271	-0.101749723608	1.3234238908	0.0166242142323	0.0430072906648	0.0628482945239	0.156682099154	0.0375336309344	-0.178604465446	-0.137485830799	0.0781771335005	-0.042136609448	0.12724238294	-0.0231450443648	0.00927028987454	0.134279382331	-0.0276260592505	0.143307494905	-23.0408262806	-12.4970925562	-4.85741699077
123	1.34950092733	-0.670908178683	0.0567200936104	0.850767305566	0.286965036168	1.72936918225	0.0409234120752	-0.253622080741	0.0674298823242	0.311156828411	-0.0487353662007	0.181365512021	-0.029798766243	-0.169933152251	0.00821117681492	0.193983027923	-0.0105162281654	0.071942837818	0.18302642579	-0.0292769633194	0.169425883957	-35.395087436	-5.57562093146	2.43593772453
124	3.75694405659	2.07864473616	0.959061128246	2.80348614785	0.909446502629	3.09260034926	0.0524453120874	-0.507366223241	0.303780052068	0.408117311883	-0.0543109660918	0.219371378413	-0.182268717908	-0.311249975759	-0.0144746910035	0.417339423291	0.0244841910938	0.075132532168	0.268760117512	-0.0488729989966	0.0870114398705	-32.9651936683	-6.02070048082	16.442948478
125	2.10835355001	0.423823686781	-0.0809706951461	2.37793113731	-0.185654624721	1.41485138292	-0.0909023814553	0.0138327987658	0.00515085063983	-0.334837046314	0.141222487065	0.0913405359028	-0.0203019918295	0.022094901505	-0.0840947453612	0.175806914953	0.0132442433285	-0.0428029380965	0.126566252077	0.0140300253788	0.127421734636	-43.4343926494	-28.3532688685	-26.6485491836
126	3.41328485643	0.698299247451	-0.280435985718	2.33723555418	-0.931664374342	4.34027139764	-0.0311122146448	0.133621766046	0.161142971359	-0.439944142674	-0.062489749557	-0.170405593408	-0.0489533026128	0.199683659935	0.0488674955218	0.164515131396	0.0486712465634	0.0207514913426	0.128696507809	0.0117210211749	0.136893275375	-36.4952893446	-35.9871155681	-25.0620283645
127	3.2091418828	1.08460860773	2.51505013327	7.48457029267	-4.85781813387	6.55099351941	-0.352706450107	0.707231001351	-0.142532629935	-0.886299092441	-0.0198577652963	-0.612866241239	0.449553072927	0.786586477085	0.2550781218	0.611305570779	-0.00545634577499	-0.00475736589248	0.298846136007	-0.0428970441203	0.208342459364	-42.9865697998	-42.5364404989	-38.6389517746
128	0.598902594563	-0.16232335943	-0.10569338773	0.0608306858099	0.112078809504	0.447089201305	0.0240088786521	0.0923816826449	-0.0967832305082	-0.25197186972	0.00913706957447	0.429371403125	0.0541776531271	-0.145251179287	-0.126023818668	0.223268987428	-0.0304862309421	-0.160853353589	0.206794297958	0.0601054121675	0.358919851077	-58.2846983856	-29.0181843284	-27.8944750311
129	0.182829459746	-0.0184078114201	0.161735228062	0.0276534919081	-0.086024825316	0.332251404969	0.0527994163305	0.157425710711	-0.00420784076766	-0.214045408414	-0.024522166374	0.155435669211	0.107139873696	-0.138497965472	-0.0623870137099	0.410686204409	-0.0281759189862	-0.383247082854	0.268908631121	0.126268851829	0.427655443949	-61.8763191463	-30.5045761999	-37.1725735173
130	0.991260398899	0.553962230077	0.127635523122	1.5289572979	-0.153784257231	1.055504273	-0.00787632116205	0.00852018137312	0.118776843788	-0.128266529602	0.0513918260089	0.147308251759	-0.137325153831	0.0611239080007	-0.0482834949632	0.144592653309	-0.00760015979573	0.0164752990797	0.142667066609	-0.000111354248007	0.138946452765	-34.946249365	-9.19598169362	-20.9204774406
131	3.69801964634	-2.49394313972	1.23938118523	2.4463767638	-1.29361739732	3.63245698174	0.117711844836	0.363612208246	0.23708027972	-0.337382904621	-0.0749968761727	-0.153690186421	-0.225298238478	0.369560074949	0.0269174406432	0.431055306737	-0.104859605776	0.02124256895	0.215513524221	0.00767817410477	0.0758194294184	-29.9806261593	-4.785548501	-39.012289654

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 6 through 66 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 67 through 96 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 97 through 141 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 142 through 255 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 256 through 392 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 393 through 420 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 6 through 66 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 67 through 96 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 97 through 141 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 142 through 200 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 201 through 255 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 256 through 304 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 305 through 392 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 393 through 420 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 6 through 66 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 67 through 96 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 97 through 141 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 142 through 255 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 256 through 392 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 393 through 420 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 6 through 66 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 67 through 90 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 91 through 124 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 125 through 255 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 256 through 304 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 305 through 392 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 393 through 420 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 6 through 66 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 67 through 96 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 97 through 141 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 142 through 254 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 255 through 392 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 393 through 420 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 6 through 66 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 67 through 96 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 97 through 141 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 142 through 255 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 256 through 392 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 393 through 420 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 6 through 66 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 67 through 96 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 97 through 141 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 142 through 170 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 171 through 200 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 201 through 304 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 305 through 392 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 393 through 420 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 6 through 66 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 67 through 96 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 97 through 124 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 125 through 255 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 256 through 331 )
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 332 through 392 )
54	X-RAY DIFFRACTION	54	chain 'G' and (resid 393 through 420 )
55	X-RAY DIFFRACTION	55	chain 'I' and (resid 6 through 45 )
56	X-RAY DIFFRACTION	56	chain 'I' and (resid 46 through 109 )
57	X-RAY DIFFRACTION	57	chain 'I' and (resid 110 through 255 )
58	X-RAY DIFFRACTION	58	chain 'I' and (resid 256 through 392 )
59	X-RAY DIFFRACTION	59	chain 'I' and (resid 393 through 420 )
60	X-RAY DIFFRACTION	60	chain 'J' and (resid 6 through 45 )
61	X-RAY DIFFRACTION	61	chain 'J' and (resid 46 through 80 )
62	X-RAY DIFFRACTION	62	chain 'J' and (resid 81 through 109 )
63	X-RAY DIFFRACTION	63	chain 'J' and (resid 110 through 170 )
64	X-RAY DIFFRACTION	64	chain 'J' and (resid 171 through 255 )
65	X-RAY DIFFRACTION	65	chain 'J' and (resid 256 through 304 )
66	X-RAY DIFFRACTION	66	chain 'J' and (resid 305 through 392 )
67	X-RAY DIFFRACTION	67	chain 'J' and (resid 393 through 420 )
68	X-RAY DIFFRACTION	68	chain 'K' and (resid 6 through 66 )
69	X-RAY DIFFRACTION	69	chain 'K' and (resid 67 through 96 )
70	X-RAY DIFFRACTION	70	chain 'K' and (resid 97 through 141 )
71	X-RAY DIFFRACTION	71	chain 'K' and (resid 142 through 225 )
72	X-RAY DIFFRACTION	72	chain 'K' and (resid 226 through 304 )
73	X-RAY DIFFRACTION	73	chain 'K' and (resid 305 through 392 )
74	X-RAY DIFFRACTION	74	chain 'K' and (resid 393 through 420 )
75	X-RAY DIFFRACTION	75	chain 'L' and (resid 6 through 66 )
76	X-RAY DIFFRACTION	76	chain 'L' and (resid 67 through 96 )
77	X-RAY DIFFRACTION	77	chain 'L' and (resid 97 through 124 )
78	X-RAY DIFFRACTION	78	chain 'L' and (resid 125 through 200 )
79	X-RAY DIFFRACTION	79	chain 'L' and (resid 201 through 254 )
80	X-RAY DIFFRACTION	80	chain 'L' and (resid 255 through 392 )
81	X-RAY DIFFRACTION	81	chain 'L' and (resid 393 through 420 )
82	X-RAY DIFFRACTION	82	chain 'M' and (resid 6 through 66 )
83	X-RAY DIFFRACTION	83	chain 'M' and (resid 67 through 96 )
84	X-RAY DIFFRACTION	84	chain 'M' and (resid 97 through 141 )
85	X-RAY DIFFRACTION	85	chain 'M' and (resid 142 through 208 )
86	X-RAY DIFFRACTION	86	chain 'M' and (resid 209 through 304 )
87	X-RAY DIFFRACTION	87	chain 'M' and (resid 305 through 392 )
88	X-RAY DIFFRACTION	88	chain 'M' and (resid 393 through 420 )
89	X-RAY DIFFRACTION	89	chain 'N' and (resid 6 through 66 )
90	X-RAY DIFFRACTION	90	chain 'N' and (resid 67 through 96 )
91	X-RAY DIFFRACTION	91	chain 'N' and (resid 97 through 124 )
92	X-RAY DIFFRACTION	92	chain 'N' and (resid 125 through 170 )
93	X-RAY DIFFRACTION	93	chain 'N' and (resid 171 through 200 )
94	X-RAY DIFFRACTION	94	chain 'N' and (resid 201 through 255 )
95	X-RAY DIFFRACTION	95	chain 'N' and (resid 256 through 304 )
96	X-RAY DIFFRACTION	96	chain 'N' and (resid 305 through 392 )
97	X-RAY DIFFRACTION	97	chain 'N' and (resid 393 through 420 )
98	X-RAY DIFFRACTION	98	chain 'O' and (resid 6 through 109 )
99	X-RAY DIFFRACTION	99	chain 'O' and (resid 110 through 420 )
100	X-RAY DIFFRACTION	100	chain 'P' and (resid 6 through 66 )
101	X-RAY DIFFRACTION	101	chain 'P' and (resid 67 through 124 )
102	X-RAY DIFFRACTION	102	chain 'P' and (resid 125 through 255 )
103	X-RAY DIFFRACTION	103	chain 'P' and (resid 256 through 392 )
104	X-RAY DIFFRACTION	104	chain 'P' and (resid 393 through 420 )
105	X-RAY DIFFRACTION	105	chain 'Q' and (resid 6 through 66 )
106	X-RAY DIFFRACTION	106	chain 'Q' and (resid 67 through 96 )
107	X-RAY DIFFRACTION	107	chain 'Q' and (resid 97 through 124 )
108	X-RAY DIFFRACTION	108	chain 'Q' and (resid 125 through 171 )
109	X-RAY DIFFRACTION	109	chain 'Q' and (resid 172 through 255 )
110	X-RAY DIFFRACTION	110	chain 'Q' and (resid 256 through 392 )
111	X-RAY DIFFRACTION	111	chain 'Q' and (resid 393 through 420 )
112	X-RAY DIFFRACTION	112	chain 'R' and (resid 6 through 66 )
113	X-RAY DIFFRACTION	113	chain 'R' and (resid 67 through 96 )
114	X-RAY DIFFRACTION	114	chain 'R' and (resid 97 through 124 )
115	X-RAY DIFFRACTION	115	chain 'R' and (resid 125 through 255 )
116	X-RAY DIFFRACTION	116	chain 'R' and (resid 256 through 392 )
117	X-RAY DIFFRACTION	117	chain 'R' and (resid 393 through 420 )
118	X-RAY DIFFRACTION	118	chain 'V' and (resid 6 through 66 )
119	X-RAY DIFFRACTION	119	chain 'V' and (resid 67 through 96 )
120	X-RAY DIFFRACTION	120	chain 'V' and (resid 97 through 124 )
121	X-RAY DIFFRACTION	121	chain 'V' and (resid 125 through 255 )
122	X-RAY DIFFRACTION	122	chain 'V' and (resid 256 through 331 )
123	X-RAY DIFFRACTION	123	chain 'V' and (resid 332 through 392 )
124	X-RAY DIFFRACTION	124	chain 'V' and (resid 393 through 420 )
125	X-RAY DIFFRACTION	125	chain 'T' and (resid 6 through 66 )
126	X-RAY DIFFRACTION	126	chain 'T' and (resid 67 through 96 )
127	X-RAY DIFFRACTION	127	chain 'T' and (resid 97 through 124 )
128	X-RAY DIFFRACTION	128	chain 'T' and (resid 125 through 171 )
129	X-RAY DIFFRACTION	129	chain 'T' and (resid 172 through 254 )
130	X-RAY DIFFRACTION	130	chain 'T' and (resid 255 through 392 )
131	X-RAY DIFFRACTION	131	chain 'T' and (resid 393 through 420 )

+
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

-
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)