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万見

- PDB-6v9a: Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72D -

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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: 6v9a

タイトル

Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72D

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: 2.3 Å

データ登録者

Zheng, Y. / 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	6v9a.cif.gz	3.9 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6v9a.ent.gz	2.7 MB	表示	PDB形式
PDBx/mmJSON形式	6v9a.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	6v9a_validation.pdf.gz	324.2 KB	表示	wwPDB検証レポート
文書・詳細版	6v9a_full_validation.pdf.gz	343.7 KB	表示
XML形式データ	6v9a_validation.xml.gz	6.6 KB	表示
CIF形式データ	6v9a_validation.cif.gz	102.8 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/v9/6v9a ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v9a	HTTPS FTP

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関連構造データ

関連構造データ	6v96C 6v99C 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	6v96-5 6v96-1 6v99-5 5w5t-2 5w6j-1 6v96-4 6v99-2 5w6j-5 5w5r-2 6v99-3 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)	92.231, 141.404, 228.648
Angle α, β, γ (deg.)	107.998, 101.626, 90.019
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: 49300.516 Da / 分子数: 20 / 変異: S72D / 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: 3971 / 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: 2.81 Å³/Da / 溶媒含有率: 56.24 %
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 / Temp details: room temperature

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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: 0.9787 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: 0.9787 Å / 相対比: 1
反射	解像度: 2.3→77.26 Å / Num. obs: 465495 / % possible obs: 98 % / 冗長度: 3 % / B_iso Wilson estimate: 38.4 Å² / R_pim(I) all: 0.083 / R_rim(I) all: 0.145 / Net I/σ(I): 4
反射シェル	解像度: 2.3→5.54 Å / Num. unique obs: 33456 / CC_1/2: 0.795

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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: 2.3→62.5 Å / SU ML: 0.295 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 33.72

	R_factor	反射数	%反射
R_free	0.2787	23598	5.07 %
R_work	0.234	-	-
obs	0.2363	465487	97.57 %

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: 41.64 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.3→62.5 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	64893	0	392	3971	69256

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0049876332414	67760
X-RAY DIFFRACTION	f_angle_d	0.763406204476	92197
X-RAY DIFFRACTION	f_chiral_restr	0.0502118140553	10021
X-RAY DIFFRACTION	f_plane_restr	0.00510974376914	12160
X-RAY DIFFRACTION	f_dihedral_angle_d	8.02502712941	55209

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 (%)
2.3261-2.3535	0.3444	823	0.2783	14562	X-RAY DIFFRACTION	97.0478773734
2.3535-2.3822	0.319788371639	792	0.273575937424	14698	X-RAY DIFFRACTION	97.0551378446
2.3822-2.4124	0.377240260725	839	0.284498407077	14694	X-RAY DIFFRACTION	97.2392638037
2.4124-2.4441	0.310491394363	787	0.27142129199	14556	X-RAY DIFFRACTION	97.2984970512
2.4441-2.4776	0.31732113582	768	0.268987939032	14689	X-RAY DIFFRACTION	97.4590163934
2.4776-2.513	0.326066402136	844	0.268906863939	14756	X-RAY DIFFRACTION	97.4512743628
2.513-2.5505	0.340963660231	912	0.277256788694	14592	X-RAY DIFFRACTION	97.5646592411
2.5505-2.5904	0.32326412167	696	0.273244087317	14818	X-RAY DIFFRACTION	97.6952141058
2.5904-2.6328	0.327863798373	828	0.264729917654	14808	X-RAY DIFFRACTION	97.7311081943
2.6328-2.6782	0.32753867774	735	0.269085730677	14705	X-RAY DIFFRACTION	97.8019889783
2.6782-2.7269	0.311312890574	770	0.281968262874	14849	X-RAY DIFFRACTION	97.7531605958
2.7269-2.7794	0.335954647879	710	0.26496490684	14785	X-RAY DIFFRACTION	98.0137896135
2.7794-2.8361	0.316843701805	700	0.267808342304	14732	X-RAY DIFFRACTION	97.5412426522
2.8361-2.8978	0.313605871231	790	0.261459072966	14907	X-RAY DIFFRACTION	97.6728268309
2.8978-2.9652	0.299125993762	721	0.255875679494	14807	X-RAY DIFFRACTION	97.7402908038
2.9652-3.0393	0.279171726113	779	0.256177764748	14697	X-RAY DIFFRACTION	98.0362346383
3.0393-3.1215	0.317371740528	791	0.252237247394	14874	X-RAY DIFFRACTION	98.280946107
3.1215-3.2134	0.295314072481	792	0.247598210123	14921	X-RAY DIFFRACTION	98.3168564635
3.2134-3.3171	0.318121540585	822	0.254010389157	14864	X-RAY DIFFRACTION	98.561105875
3.3171-3.4356	0.323015563382	806	0.244178782967	14742	X-RAY DIFFRACTION	98.3179461237
3.4356-3.5732	0.268882826394	852	0.225260158794	14949	X-RAY DIFFRACTION	98.6699138254
3.5732-3.7358	0.224164101087	752	0.21295884884	14871	X-RAY DIFFRACTION	98.7048268891
3.7358-3.9327	0.221153837138	887	0.202731510797	14827	X-RAY DIFFRACTION	98.5141997367
3.9-4.9	0.309960362303	765	0.282007032771	14713	X-RAY DIFFRACTION	97.095539803
3.9327-4.179	0.229498967109	781	0.192918179748	14931	X-RAY DIFFRACTION	98.730677391
4.179-4.5016	0.22839012827	809	0.183504665121	14763	X-RAY DIFFRACTION	98.6256254354
4.5016-4.9545	0.24501188548	783	0.184572780747	14984	X-RAY DIFFRACTION	98.6917876815
4.9545-5.671	0.248000461656	685	0.206574532483	14999	X-RAY DIFFRACTION	98.8528929787
5.671-7.1432	0.243634768218	833	0.224939565698	14963	X-RAY DIFFRACTION	99.0096527517
7.1432-62.5	0.230402739935	748	0.203575399108	12839	X-RAY DIFFRACTION	85.5981855982

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	1.36126038425	0.398613894808	0.0589380563436	3.08260754829	0.221663809403	1.03216474431	-0.0465287222041	-0.070415417378	-0.00701783477563	-0.40559457895	0.12053287087	0.0320157266586	-0.0326955865312	-0.0330365909093	-0.0704314181406	0.325475861131	0.032211206812	0.0448644651554	0.324763565953	-0.0113867727004	0.178198379018	23.8852720412	25.1182641566	17.1753457455
2	1.63888748633	1.40217984218	-0.510561958703	5.63323391989	0.79155272645	4.92465639516	-0.125184069883	0.18935297909	0.395458344393	-0.980019881073	0.162681782619	0.47590143271	-0.719156302475	-0.31286011535	-0.0319885592408	0.455515484196	0.0610308563977	0.0978141162232	0.282258286221	0.025836889764	0.39495122439	29.4175809126	32.4113706824	9.50270105443
3	1.12058789158	-0.726787185879	-0.459578239165	0.624454002136	0.511392305324	0.784051644595	-0.0305075633746	-0.0455862309286	0.0509968004688	-0.444540905661	0.0605870597892	-0.595091764816	0.0678137930054	0.367719558615	-0.0198057414896	0.452031410094	0.011352931187	0.294718871079	0.406058443127	-0.0412125951033	0.726671934625	45.589519179	22.3916129698	9.96750442942
4	1.02842202337	0.222043756624	-0.107601399547	1.26949756861	-0.264085542691	1.1013885216	-0.0584950025069	-0.137128979102	0.0785660571477	-0.499746760482	0.0760144071848	-0.582294626428	0.0483388693156	0.10182594762	-0.0186021399417	0.419803947528	0.0709276511381	0.155273785604	0.344720433674	-0.0370126582909	0.368843898369	34.3612750453	15.9690160783	16.7269670626
5	1.09481724802	0.0796583773411	0.0672905171353	1.105938095	0.107939612319	1.44913577222	0.0295788934149	-0.2304980091	-0.151942630043	-0.311009677087	-0.0593390916803	0.247273072999	0.227154159317	-0.368990976343	0.00472590396039	0.392719512512	-0.00473045667894	-0.13328017411	0.426578280215	0.049377841728	0.243106652433	10.4383460912	-1.20881588456	21.4985038875
6	4.57230856315	-3.12704666777	-1.78484178157	4.17103991862	1.48353420554	3.54579506034	0.0480000283909	0.672724380738	-0.419021080311	-0.504215375406	-0.115843281721	0.292395218932	0.383669459712	-0.28918997084	0.041867280098	0.859393148902	-0.0422158717062	-0.128392262299	0.37223061502	-0.0128548272286	0.271993544117	13.5519578444	-1.35290210501	3.96315139177
7	1.35318511033	-0.310042785766	0.47801286428	2.87341252902	-0.728615584744	1.35941799127	0.118481513731	-0.0694595500006	0.04181961003	-0.609316113395	-0.00880268217061	-0.0826249901386	-0.0318119737337	-0.00312972587211	-0.109565204703	0.414980020421	0.0176454827826	-0.0037358894301	0.181304802568	0.00144090076538	0.248118411943	-41.2042098759	-30.8340213215	59.7961133566
8	1.67943122385	1.07869654815	0.582630238958	4.99682824047	-0.586784122695	3.39905673648	0.0736102785663	0.314567129672	-0.4716445788	-1.08895156555	-0.0132181202115	-0.347757479071	0.518103045974	0.317256990724	-0.0736104702153	0.711479072445	0.120692097927	-0.118437652309	0.320857883612	-0.0155875566773	0.363493719828	-46.9861504856	-38.3690301216	52.4152891685
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83	1.82748180274	-0.142318441523	-0.470145367711	1.3547350025	0.678672663704	1.80899559482	0.0356542233521	0.207371128174	0.135180072829	0.337951017156	0.063100453557	-0.119234264048	-0.172167083591	-0.265297417076	-0.0764379865599	0.344038542189	0.0449829696629	0.0394966055523	0.175411986192	0.0293148506758	0.248344055414	10.1854613228	-75.37259103	40.0515472523
84	7.19159021966	4.8393213639	1.38847821945	6.54200597033	1.40614002632	3.35376852485	-0.0238949831257	-0.698366274037	0.459732321627	0.524158969544	-0.00251058273385	0.309451299376	-0.270070225417	-0.351991214655	0.012476058585	0.720433661579	0.159662025357	0.0369141326615	0.316857696341	-0.00902952212487	0.240959808229	12.8576505026	-75.2543875684	57.6945626103
85	1.28102066799	0.0455297665639	0.0693249412436	2.12026847673	-0.33814375524	1.27030608497	0.200171988811	0.139766524494	0.00840197693852	0.00428638918525	-0.0547862861149	-0.203829242449	0.140831595423	0.112262053159	-0.106027901614	0.254762139226	0.0427785390354	-0.0325372734482	0.157218741465	0.00906657307774	0.310251204379	5.95036239292	-102.147373469	101.326855186
86	1.92916298666	1.51479693618	1.54323817916	7.81933961441	-2.74080954932	4.77780182924	-0.0798496809446	0.477919244398	-0.601313006799	-1.14277474788	-0.169541459362	-1.0183653948	0.655394667037	0.736595763065	0.252301666053	0.58298269574	0.176935072999	0.0133554835856	0.373175799574	-0.0866866021991	0.484578836797	4.47873933481	-113.99503781	88.9516935131
87	1.19690436201	-0.137577064002	0.237462959597	1.2220007717	-0.273435014244	1.09354974673	0.227784545532	0.185230060219	-0.125202927242	-0.313032042675	-0.0193761222389	0.387344580139	0.108191117376	-0.143016633274	-0.181007744219	0.306728650866	0.0602008882289	-0.0703975157581	0.182285170753	0.0356384325416	0.337416283218	-13.3847017102	-101.402283957	92.8196330196
88	0.261655369367	0.00283973453383	0.0315438503347	0.57562600594	-0.0738287989392	0.298224887525	0.106926540507	-0.000834873146003	0.264161918783	0.0872476518824	-0.00938453937811	-0.0117890779419	-0.137464172988	0.0203379357478	-0.00804286672802	0.346352421159	0.0160950100019	0.126860270889	0.0345193172285	0.0352622986305	0.542855619788	11.6715461535	-80.165644904	106.085005855
89	3.05749371076	-2.51103778346	1.30037033609	5.79354725101	-0.190436617277	4.73928632863	-0.0959988961527	0.629532650819	0.438559254681	-0.382879958544	0.0799871634618	-0.397376830972	-0.33669752761	0.351409979837	0.0156419379647	0.329373323593	0.039999604425	0.175685545142	0.346302001981	0.13546350751	0.437831214092	16.9093463317	-76.1554452456	88.1621392144
90	2.15834043051	-0.846313776662	0.476818724366	3.50143353534	0.858392999293	1.23399216231	0.171360534318	-0.29140278259	-0.165485035243	0.120093416642	-0.0248311735686	0.360022934078	0.293669660074	-0.116267685746	-0.106167502577	0.260601766103	-0.0493838977338	0.00179016308737	0.160284276611	0.0103366557951	0.33099738127	23.7373138128	-105.043774283	133.226241734
91	0.883504204521	-0.23042780326	0.0624478274091	0.869905681332	-0.0999660605499	0.588076399899	0.147087605081	-0.0763976556241	0.197680045589	0.0462553785258	-0.0686502980231	-0.100511441419	-0.03628270324	0.116426454481	-0.0633536889403	0.24567283245	-0.0228386810276	0.0432876834304	0.107269432253	-0.0371214491417	0.325162523406	29.848034759	-90.5436922941	131.960039845
92	2.92963547449	2.4259255272	0.819854049849	5.53612922844	-0.344941061313	5.09904440422	-0.163789257546	-0.551905257863	0.456393801823	0.361114354996	0.0677235600516	0.268778249735	-0.344659825036	-0.402027534459	0.0317016915712	0.259963490133	-0.0110925444197	0.118411127097	0.355108685038	-0.128785859316	0.424308342627	12.3245761957	-76.0584998779	143.391460631
93	1.36889194692	0.145197698361	0.688523840493	3.79115250697	0.437023949674	1.51295478889	0.115190016099	0.0562057751014	-0.038483775916	0.567923853411	-0.0266273319688	-0.109010814595	0.043416716723	0.0548919333746	-0.0888004657404	0.288580455441	0.00693500281926	-0.0523015392807	0.341151212336	0.00491126094609	0.194152533243	-21.7301457431	-31.8600719828	2.50420638648
94	4.20832216091	-1.99047083352	0.412826344539	6.10456927099	1.93001876667	5.06458423256	-0.161493670479	-0.488687770884	-0.47115466644	1.12179049216	0.0388931376179	0.560824602566	0.721005551007	-0.397899084244	0.154266375806	0.983302613917	-0.0497516260121	-0.177477322589	0.318695155711	0.0626292931792	0.485052807732	-19.9473204039	-43.7354353233	14.412087583
95	0.922343531289	0.23965693839	0.327165407451	0.109834815318	0.230629383144	0.589393905033	0.0918100602239	0.0333789906138	-0.244148317081	0.746443583409	-0.0775695231578	-0.785236950053	0.239075403734	0.208249983549	-0.0503443104489	0.578908378804	0.020243086913	-0.355985544767	0.328685201333	-0.0222700471381	0.859625860076	-2.22044000633	-31.1932127329	10.45570764
96	1.37744851568	0.373695689674	0.417698751164	2.76968390932	0.284338030866	1.24411689093	-0.0767556798365	0.224918056408	-0.0356463138803	0.218396458913	0.202314061131	-0.578070811519	-0.057409466528	0.0417668989028	-0.112508393267	0.25214845682	0.0169088365373	-0.0686864867079	0.409377702429	-0.0336235938915	0.247158044993	-16.1848397217	-16.2601339576	-2.36584929848
97	1.10628127168	-0.129967254175	-0.328582911183	0.928573073798	0.678745949553	1.85157784701	0.134841960468	-0.0962689028294	0.103228085304	0.36588813252	-0.0140025438805	0.199233105452	-0.0991791739158	-0.159022047769	-0.105275354643	0.291261656066	0.0114035190833	0.0994698648185	0.468173250244	0.0206698128456	0.215286481711	-35.2937412678	-5.41750874538	-0.74500596587
98	5.95630746378	3.99113536319	2.03339477995	5.42291651517	1.35481222139	3.89794703863	0.0186952443773	-0.661943195464	0.525391017545	0.531265656715	-0.142906972003	0.372167851091	-0.189430011848	-0.398941688639	0.10305566563	0.734418322726	0.0369265400866	0.118376189072	0.321011085774	-0.0350419627321	0.257888921989	-32.5235003014	-6.21760785858	16.7765214852
99	1.12069765793	-0.0546620738629	0.0567299918652	2.96747561788	-0.325358910763	1.10263719255	-0.0477173894988	-0.119459896162	0.0988048974065	-0.438941761389	0.116507953111	-0.00646545289293	0.0484954895992	0.00614149377995	-0.0629149223455	0.328988880642	0.0327576820047	-0.0618284084156	0.202195315772	0.0276459728842	0.249759910028	-40.3794677014	-31.1097689549	-25.6567625405
100	4.33154037636	0.895572594739	1.77061622444	7.55173268572	-3.43879641901	8.43713334229	-0.116749692454	0.709261908199	-0.334993631618	-1.46461286548	0.101269479147	-0.119423189139	0.666428845723	0.857672614318	0.0472282329682	0.759916761011	-0.0302989678539	-0.0773056912107	0.349238796383	-0.0111774375253	0.410781331223	-42.2796287893	-42.2357046182	-38.1976690005
101	0.498891828395	-0.519634285391	0.128797859995	0.797129352684	-0.454898247453	0.440148138758	0.0133331328752	0.166298765467	-0.0583908040767	-0.661985963011	0.0160753194415	0.723550074437	0.114484428819	-0.243640512542	-0.118178319597	0.526584040738	0.0103155835648	-0.302444749956	0.294711290089	0.0855871762319	0.747755323499	-59.8622013301	-29.8408781113	-33.4270745255
102	1.17514270856	-0.122209362665	-0.0553947717813	2.06374790961	-0.256472867502	1.32271025492	-0.0445514767425	-0.212003522245	0.102768103158	-0.152266982366	0.205968085201	0.669037579334	-0.144494813598	-0.0296577889457	-0.128968873323	0.281256927517	0.0240392060803	-0.0313262642285	0.252603033614	0.0620957000894	0.339704047168	-46.0485252531	-15.753999665	-19.8294501726
103	2.05589601822	0.179234552713	-0.375784372207	1.56006396898	-0.427165207042	1.92419258906	-0.114232572743	-0.275387609287	0.173952386746	-0.294398207425	0.0843421277514	0.0733127147518	-0.12713302542	0.211094873832	-0.0177936833562	0.310966170246	-0.0151384273828	0.0592757493002	0.201154268337	-0.00654207174632	0.233115307989	-27.0226829898	-4.71137569026	-20.9416264094
104	5.50754101381	-3.84720105417	1.54106585404	6.21515385724	-1.94643521915	4.51210712129	0.0727568289368	0.721879724856	0.474750888862	-0.486564938255	-0.0245494474553	-0.307527275415	-0.292097035451	0.419434005846	-0.0130307042545	0.581395670172	-0.0844486976437	0.0723711075599	0.381125603227	0.0456280940619	0.226031247963	-29.5990944253	-4.63179559917	-38.5966950397

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 96 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 97 through 141 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 142 through 225 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 226 through 304 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 305 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 96 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 97 through 141 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 142 through 392 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 393 through 420 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 6 through 96 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 97 through 141 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 142 through 304 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 305 through 392 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 393 through 420 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 6 through 90 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 91 through 141 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 142 through 255 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 256 through 392 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 393 through 420 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 6 through 96 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 97 through 141 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 142 through 200 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 201 through 255 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 256 through 392 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 393 through 420 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 6 through 66 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 67 through 96 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 97 through 141 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 142 through 304 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 305 through 392 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 393 through 420 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 6 through 66 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 67 through 96 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 97 through 124 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 125 through 304 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 305 through 392 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 393 through 420 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 6 through 95 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 96 through 124 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 125 through 304 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 305 through 392 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 393 through 420 )
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 6 through 66 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 67 through 124 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 125 through 331 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 332 through 392 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 393 through 420 )
49	X-RAY DIFFRACTION	49	chain 'J' and (resid 6 through 45 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 46 through 80 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 81 through 124 )
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 125 through 225 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 226 through 304 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 305 through 392 )
55	X-RAY DIFFRACTION	55	chain 'J' and (resid 393 through 420 )
56	X-RAY DIFFRACTION	56	chain 'K' and (resid 6 through 96 )
57	X-RAY DIFFRACTION	57	chain 'K' and (resid 97 through 141 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 142 through 255 )
59	X-RAY DIFFRACTION	59	chain 'K' and (resid 256 through 392 )
60	X-RAY DIFFRACTION	60	chain 'K' and (resid 393 through 420 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 6 through 80 )
62	X-RAY DIFFRACTION	62	chain 'L' and (resid 81 through 109 )
63	X-RAY DIFFRACTION	63	chain 'L' and (resid 110 through 304 )
64	X-RAY DIFFRACTION	64	chain 'L' and (resid 305 through 392 )
65	X-RAY DIFFRACTION	65	chain 'L' and (resid 393 through 420 )
66	X-RAY DIFFRACTION	66	chain 'M' and (resid 6 through 80 )
67	X-RAY DIFFRACTION	67	chain 'M' and (resid 81 through 109 )
68	X-RAY DIFFRACTION	68	chain 'M' and (resid 110 through 370 )
69	X-RAY DIFFRACTION	69	chain 'M' and (resid 371 through 420 )
70	X-RAY DIFFRACTION	70	chain 'N' and (resid 6 through 96 )
71	X-RAY DIFFRACTION	71	chain 'N' and (resid 97 through 141 )
72	X-RAY DIFFRACTION	72	chain 'N' and (resid 142 through 392 )
73	X-RAY DIFFRACTION	73	chain 'N' and (resid 393 through 420 )
74	X-RAY DIFFRACTION	74	chain 'O' and (resid 6 through 96 )
75	X-RAY DIFFRACTION	75	chain 'O' and (resid 97 through 141 )
76	X-RAY DIFFRACTION	76	chain 'O' and (resid 142 through 392 )
77	X-RAY DIFFRACTION	77	chain 'O' and (resid 393 through 420 )
78	X-RAY DIFFRACTION	78	chain 'P' and (resid 6 through 57 )
79	X-RAY DIFFRACTION	79	chain 'P' and (resid 58 through 96 )
80	X-RAY DIFFRACTION	80	chain 'P' and (resid 97 through 141 )
81	X-RAY DIFFRACTION	81	chain 'P' and (resid 142 through 255 )
82	X-RAY DIFFRACTION	82	chain 'P' and (resid 256 through 304 )
83	X-RAY DIFFRACTION	83	chain 'P' and (resid 305 through 392 )
84	X-RAY DIFFRACTION	84	chain 'P' and (resid 393 through 420 )
85	X-RAY DIFFRACTION	85	chain 'Q' and (resid 6 through 96 )
86	X-RAY DIFFRACTION	86	chain 'Q' and (resid 97 through 124 )
87	X-RAY DIFFRACTION	87	chain 'Q' and (resid 125 through 255 )
88	X-RAY DIFFRACTION	88	chain 'Q' and (resid 256 through 392 )
89	X-RAY DIFFRACTION	89	chain 'Q' and (resid 393 through 420 )
90	X-RAY DIFFRACTION	90	chain 'R' and (resid 6 through 124 )
91	X-RAY DIFFRACTION	91	chain 'R' and (resid 125 through 392 )
92	X-RAY DIFFRACTION	92	chain 'R' and (resid 393 through 420 )
93	X-RAY DIFFRACTION	93	chain 'V' and (resid 6 through 95 )
94	X-RAY DIFFRACTION	94	chain 'V' and (resid 96 through 124 )
95	X-RAY DIFFRACTION	95	chain 'V' and (resid 125 through 255 )
96	X-RAY DIFFRACTION	96	chain 'V' and (resid 256 through 304 )
97	X-RAY DIFFRACTION	97	chain 'V' and (resid 305 through 392 )
98	X-RAY DIFFRACTION	98	chain 'V' and (resid 393 through 420 )
99	X-RAY DIFFRACTION	99	chain 'T' and (resid 6 through 96 )
100	X-RAY DIFFRACTION	100	chain 'T' and (resid 97 through 124 )
101	X-RAY DIFFRACTION	101	chain 'T' and (resid 125 through 255 )
102	X-RAY DIFFRACTION	102	chain 'T' and (resid 256 through 304 )
103	X-RAY DIFFRACTION	103	chain 'T' and (resid 305 through 392 )
104	X-RAY DIFFRACTION	104	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://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

+
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)