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万見

- PDB-6v99: Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase- S72D in ... -

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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: 6v99

タイトル

Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase- S72D in the presence of sulfate

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: 2.287 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	6v99.cif.gz	3.9 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6v99.ent.gz	2.7 MB	表示	PDB形式
PDBx/mmJSON形式	6v99.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/v9/6v99 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v99	HTTPS FTP

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関連構造データ

関連構造データ	6v96C 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 6v96-5 6v96-4 6v96-3 5w6j-4 6v96-1 5w5r-4 6v96-2 5w5t-2 6v9a-4 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

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

H: 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

W: Glucose-1-phosphate adenylyltransferase

T: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

999 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)

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

登録者が定義した集合体
根拠: gel filtration
200 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)

Q: Glucose-1-phosphate adenylyltransferase

R: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

E: Glucose-1-phosphate adenylyltransferase

F: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者が定義した集合体
200 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)

O: Glucose-1-phosphate adenylyltransferase

P: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

G: Glucose-1-phosphate adenylyltransferase

H: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者が定義した集合体
200 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

登録者が定義した集合体
200 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

W: Glucose-1-phosphate adenylyltransferase

T: Glucose-1-phosphate adenylyltransferase

ヘテロ分子

登録者が定義した集合体
200 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)	93.416, 141.581, 228.316
Angle α, β, γ (deg.)	108.067, 101.846, 89.998
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-SO4 / SULFATE ION / 硫酸ジアニオン分子量: 96.063 Da / 分子数: 136 / 由来タイプ: 合成 / 式: SO₄
#3: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 2590 / 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: 2.84 Å³/Da / 溶媒含有率: 56.73 %
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: Lithium sulfate, Tris, PEG 400 / 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: 2.28→72.74 Å / Num. obs: 478212 / % possible obs: 98.1 % / 冗長度: 2 % / B_iso Wilson estimate: 23.24 Å² / R_pim(I) all: 0.066 / R_rim(I) all: 0.093 / Net I/σ(I): 5.6
反射シェル	解像度: 2.28→6.21 Å / Num. unique obs: 22545 / CC_1/2: 0.648

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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: 2.287→72.7 Å / SU ML: 0.342658826812 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 30.029

	R_factor	反射数	%反射
R_free	0.2543	24319	5.09 %
R_work	0.2084	-	-
obs	0.2107	478200	97.46 %

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: 57.5084519255 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.287→72.7 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	64749	0	680	2590	68019

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.00798302586147	67146
X-RAY DIFFRACTION	f_angle_d	0.939662804633	91420
X-RAY DIFFRACTION	f_chiral_restr	0.055738358575	9945
X-RAY DIFFRACTION	f_plane_restr	0.00600809070959	11943
X-RAY DIFFRACTION	f_dihedral_angle_d	6.86592441692	54589

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 (%)
2.3131-2.3403	0.3508	773	0.3041	15060	X-RAY DIFFRACTION	96.9327782539
2.3403-2.3689	0.353927728872	829	0.293964219563	15063	X-RAY DIFFRACTION	97.3595540036
2.3689-2.3989	0.361539132014	742	0.285768928247	15379	X-RAY DIFFRACTION	97.3666727064
2.3989-2.4304	0.33989321526	819	0.282321948019	14984	X-RAY DIFFRACTION	97.3990755008
2.4304-2.4637	0.31935986057	855	0.284798290094	15009	X-RAY DIFFRACTION	96.8379929191
2.4637-2.4989	0.311376961752	823	0.263264734675	15011	X-RAY DIFFRACTION	97.5540632124
2.4989-2.5362	0.309121554834	777	0.258877641694	15387	X-RAY DIFFRACTION	97.7681001633
2.5362-2.5758	0.326985529414	814	0.257482420818	15169	X-RAY DIFFRACTION	97.8271514261
2.5758-2.6181	0.311836672677	786	0.25643794412	15194	X-RAY DIFFRACTION	97.6235567231
2.6181-2.6632	0.333061485104	792	0.287140038272	15053	X-RAY DIFFRACTION	96.6217452284
2.6632-2.7117	0.321558419523	869	0.264237547988	15015	X-RAY DIFFRACTION	97.7597242738
2.7117-2.7638	0.280303019847	722	0.244934967299	15263	X-RAY DIFFRACTION	97.9713164991
2.7638-2.8202	0.282876773861	795	0.244632242497	15295	X-RAY DIFFRACTION	98.0201035638
2.8202-2.8816	0.320704823482	744	0.245225923225	15273	X-RAY DIFFRACTION	97.981280969
2.8816-2.9486	0.276426071863	847	0.23590273557	15120	X-RAY DIFFRACTION	97.9029983445
2.9486-3.0223	0.284266358811	929	0.225055222676	15230	X-RAY DIFFRACTION	98.1772890212
3.0223-3.104	0.272703725714	865	0.227452976223	15148	X-RAY DIFFRACTION	98.154958931
3.104-3.1954	0.261921569734	874	0.220901126439	15233	X-RAY DIFFRACTION	98.2913284921
3.1954-3.2985	0.259567668419	919	0.213219838087	15229	X-RAY DIFFRACTION	98.5655862785
3.2985-3.4164	0.23766432689	838	0.211591270985	15228	X-RAY DIFFRACTION	98.6188693143
3.4164-3.5532	0.263486770918	818	0.193334129891	15342	X-RAY DIFFRACTION	98.7473266117
3.5532-3.7149	0.2362337721	843	0.189921152115	15352	X-RAY DIFFRACTION	98.7981942411
3.7149-3.9108	0.231396380877	870	0.176462769586	15196	X-RAY DIFFRACTION	98.691565821
3.9-4.9	0.376559298583	723	0.318684090523	13739	X-RAY DIFFRACTION	88.6314886315
3.9108-4.1558	0.201624732843	812	0.166905049597	15396	X-RAY DIFFRACTION	98.8413221125
4.1558-4.4766	0.198975862652	736	0.155958738871	15495	X-RAY DIFFRACTION	98.9272871335
4.4766-4.927	0.181111660601	771	0.15614591749	15332	X-RAY DIFFRACTION	98.9796545577
4.927-5.6397	0.235022265777	857	0.181478263111	15360	X-RAY DIFFRACTION	99.0774682307
5.6397-7.1045	0.253804135671	833	0.210030340112	15437	X-RAY DIFFRACTION	99.1287394139
7.1045-72.7	0.220005796244	644	0.193812542075	13903	X-RAY DIFFRACTION	89.0923566879

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	3.08671335391	0.837199667611	-0.98866345282	5.15231313909	-0.786016505626	2.63806937251	0.0266528883209	-0.00518723717329	-0.0787996913348	-0.702390757854	0.130859077546	-0.00682208840107	0.0141247637832	0.0538074517903	-0.191767594539	0.552588170026	0.0630301351271	-0.0750282283918	0.307008398364	0.00796245443889	0.267057901016	-44.5755152974	-28.5535549904	59.3161621701
2	6.15791300174	1.51635305682	-0.384895325145	4.82680843174	-0.0181169508374	4.88618447213	0.0863756733409	0.474311218575	0.105323992162	-0.986042859491	-0.0254157892495	-0.311268570905	-0.0394247228861	0.149647675367	-0.0111669858402	0.511790984026	0.0856122112371	0.0330166906427	0.345218817848	-0.00841090232044	0.367234379307	-37.340335404	-36.3687785303	61.1675724173
3	6.6035919897	-0.581242396128	1.4250963431	7.18529041167	-1.39151705061	7.88139418979	-0.000598191854975	1.04034114907	-0.52413910261	-1.44928484907	0.0734660081522	-0.52433682039	0.104532364337	0.960026021372	0.022194460668	1.25012639194	0.107185334686	-0.158095923301	0.66253704861	-0.127768746466	0.61041068589	-44.7632628642	-42.2217081197	47.7499301541
4	1.83040331778	0.228618662333	0.418242876428	1.5656830166	-0.416207718976	1.40452773235	0.289941187279	0.26124825573	-0.360621860995	-0.913872487055	-0.0885712578047	0.939120481178	0.145817655214	-0.469917114011	-0.15518848847	0.800267295502	0.106395319728	-0.343539927638	0.499949957007	-0.00524276230685	0.624849080582	-61.9951724045	-29.57403608	53.56942909
5	1.45707407754	0.673636078317	0.164902037813	2.84823333526	-0.557205890933	0.713963003238	0.278617490467	-0.199958374251	0.19965743376	-0.161955181263	-0.126027123685	0.339660325081	-0.664763549673	-0.109228539776	-0.190783321551	0.669564604261	0.0897537665308	0.0329961449211	0.472163919118	-0.00569044386904	0.3359854415	-47.1763445644	-15.7303149413	66.1824125044
6	1.78328190839	0.207750364711	0.615871773349	1.25263961119	-0.687971136116	2.64904911037	0.0443814989069	0.12934338359	0.350318434914	-0.03575177973	0.0474985774773	-0.0351811268606	-0.694574826471	0.488517231896	-0.0582828853209	0.713554648575	-0.103231650882	0.25004976258	0.446510062297	-0.0176232757237	0.52405591499	-27.9668283514	-4.5763695482	63.8243289622
7	4.51088615662	-1.97363687613	0.854640788616	5.03880804686	-0.18740926105	3.54527293105	-0.0090385053961	1.24057576076	0.542646096971	-0.700423321548	0.150228877862	-0.479905859177	-0.0949693105682	0.207759172369	-0.152376396667	1.01882857803	-0.000675435949473	0.252017729387	0.619152665421	0.0929480016878	0.449972559171	-31.782006835	-4.52752226318	46.2779756954
8	3.13749141291	-1.21715865604	-0.254859184557	5.17956829145	0.757511369186	2.68112606438	-0.197887319217	-0.0133950380929	-0.0618843174972	0.154921236555	0.33291952204	-0.122257348071	-0.0833060390453	0.150125572994	-0.138064898444	0.276531071956	-0.0681587752717	0.02128374435	0.321862585087	-0.0758947426994	0.347027115286	-18.262961693	-29.2181580943	88.129628362
9	1.55212314462	-1.3208188242	1.13072764478	5.74634793726	1.36583153535	3.60565535755	-0.0231688519657	-0.213731615682	-0.0340132886237	0.0589851043929	-0.155159066833	0.172337261974	-0.350168556897	-0.179784772423	0.0915143420203	0.337142976707	-0.107896418351	0.0690577466508	0.424125522157	-0.0556326928631	0.49571639469	-25.4270337812	-36.961883914	85.7757866472
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84	1.40753104448	0.958833917463	0.482510582915	0.560335522627	0.490467062579	1.43991448851	0.0804247819308	-0.110209636753	-0.0820268636539	0.526609698205	0.244200482961	-1.20906110292	0.213158764349	0.440174105634	-0.333062376193	0.581951790955	-0.0284153509945	-0.339212368447	0.529668871252	-0.154819954243	0.932446758786	44.6966282184	-96.7039388357	50.361076929
85	0.439229857281	-0.518523910613	0.49285917114	0.736715038607	-0.254594932828	1.38498581362	0.0806540694907	-0.36187696411	-0.208110417924	1.16867358893	0.161674162886	-1.3313270171	0.152001785646	0.461032419722	-0.292499185503	1.10731421592	0.031673529958	-0.556966448688	0.58900567316	-0.0624226154845	0.990940518445	41.6579781831	-107.069338826	57.0146208286
86	0.976185633806	-0.694260371532	0.389822664297	3.37874682346	-0.0476296711511	1.32514798043	0.0403270042164	0.0948246547662	0.152636986804	0.221891129728	0.0229421711683	-0.276547232502	-0.178094317318	-0.0744139648395	-0.0720165013401	0.333905225638	-0.0182303998647	0.0631561518629	0.325922724691	-0.00654256115097	0.332899859129	17.7726419309	-79.8071149572	39.8544831628
87	4.79616368553	1.15089830832	-0.803631593715	6.00218709087	0.595788247058	3.32334860819	-0.0707343573417	-1.04284205576	0.49810298776	1.10319201037	0.330212281076	0.0235967957771	-0.122773768235	-0.0409768901771	-0.288102200883	0.909870060001	0.0326663982456	0.0169799368347	0.500090584684	-0.0460192619527	0.310582967194	12.9512907599	-75.2292253519	57.9665829168
88	2.96216509199	1.20059280156	-0.246496967638	3.94513853986	-0.300097685686	1.73929650165	0.137013853988	0.0501290441761	-0.211009606621	0.0512443894347	-0.0631585688712	-0.395139890329	0.00582606256858	0.112924962273	-0.0961752147678	0.203582700627	0.100337061205	-0.0172903641054	0.323115106094	0.0123476485687	0.212800449545	3.6840064768	-98.4613990511	99.5896388495
89	3.56765803129	1.09498114254	2.73456949113	4.50503509816	-0.462205772707	3.78455069215	0.163432489717	0.515610873487	-0.396714707494	-0.380232952825	-0.058370242827	-0.443026510333	0.428503157182	0.625769807884	-0.0839657407825	0.364839090443	0.139699461045	-8.22890016233E-5	0.462905447582	-0.0506885630886	0.425102323416	6.74890615265	-110.347292188	97.0965178226
90	1.76042745956	0.684951197101	0.450922676648	1.40321466192	0.0315682252224	0.68271376236	0.0962967106754	0.166316470661	0.13133024237	-0.11096991448	-0.00462064674221	0.0410323895819	0.016827078196	0.0146625765018	-0.0822604334596	0.21660455199	0.0767140098474	0.057443073453	0.394280765326	0.0443528655496	0.239322415074	1.29063807262	-89.1121282295	98.3605602669
91	1.7861013447	-0.566478815272	-0.0568237645786	3.61546067182	0.464036759114	1.95777858051	0.0458721882904	-0.0861950451275	-0.0284809636324	0.000551401258227	0.00166961449506	0.231567667901	0.0371258350118	-0.149715447652	-0.0363265529748	0.19505517168	-0.0536768680808	0.0155534881151	0.400220773946	-0.018758339379	0.274520174667	25.9916702576	-98.3830925261	132.038065248
92	5.43335369749	-0.694894531426	1.65737669099	6.22329759997	-0.806731196089	3.41668378321	0.243317580905	-0.235496759898	-0.203842902182	-0.148873953324	-0.194570343669	0.583026475234	0.123482484737	-0.262549580989	-0.0123186916235	0.265190380483	-0.0632151438387	-0.0440930958791	0.399563581138	0.0188412221379	0.302511525676	21.1924469376	-108.019534855	128.746966804
93	1.73417831938	-1.20841409428	1.45330531929	6.24886727169	0.266649914858	2.95069816865	0.0913564880716	-0.396622611008	-0.451786683602	0.731234726985	0.178741014659	0.536317600522	0.46018727473	-0.514778619291	-0.199491778273	0.341614581482	-0.0793607618541	0.042851273751	0.463221596222	0.0451862633797	0.356148594547	28.965096894	-109.775732539	138.417589952
94	2.16748095285	0.927595142796	0.390206028762	2.97966733044	0.898032551239	1.49878890899	0.152186044602	-0.276211839295	-0.0839965156657	0.358518350865	0.0480175594792	-0.490061545472	0.191866712235	0.294081302387	-0.180318725699	0.234355254007	-0.00606849725136	-0.0463643800755	0.441412183979	-0.0731000664801	0.310378205443	44.3336029472	-100.871359509	140.217803075
95	1.3966617874	-0.870672711283	0.533191145039	1.28792680235	-0.451260419279	0.948064290673	0.082471229023	-0.0776002219821	0.27817961304	-0.0628271253931	-0.0100926643915	-0.0332729370695	-0.0755197536353	-0.0659153823382	-0.0806504810021	0.254067349143	-0.0297943402965	0.0570817036854	0.431612021205	-0.0458976471147	0.365792797134	19.0266984397	-81.071953347	123.852226893
96	1.95374078273	-0.297551320544	0.579396828491	3.90072902613	-0.265044657715	1.86746684852	0.0113536292446	-0.655812624867	0.453329104814	0.425432135312	0.0182652930928	0.210421228926	-0.118038276935	-0.436257399066	-0.0691996218138	0.24054495281	-0.0184863686994	0.109763043026	0.566944272457	-0.107108294845	0.372884169578	11.267336338	-75.6735729327	140.053715706
97	2.70410166454	-0.733114720502	-0.577026745185	4.76479956476	0.852342331303	2.12511404227	0.0962295914405	-0.128641269583	-0.0315653642931	0.874213930327	-0.0341772774116	-0.0232935504977	0.103518874301	-0.0409733414301	0.00729981268622	0.528612280415	-0.082800268033	-0.0654770368687	0.312624868295	-0.0270049344754	0.29178355774	-19.328533675	-27.9675365977	4.67388140888
98	4.72124076742	0.138228871936	1.60976998506	3.22167699808	-0.410333886156	3.49263914385	0.236392464225	-0.205414206866	0.160142055488	0.954139978769	-0.230095298426	0.154147340961	0.257984718286	-0.0827297733289	-0.0376208658216	0.626370864862	-0.122792968372	0.00252879204032	0.341152681591	-0.0399366489654	0.418834556244	-24.2969629482	-37.4172957905	1.22652509
99	1.20606452961	-1.20369500652	1.84031732557	5.64905934851	-1.22010943983	2.97570673572	0.199714623841	-0.441621169214	-0.412483275912	1.70658630982	0.298698064561	0.136168823105	0.691480912883	-0.476554907046	-0.425057513016	1.09856058065	-0.154173915285	-0.186384962991	0.501947678107	0.0368593163704	0.481035494694	-15.9982849431	-39.4886740284	10.5514669158
100	1.19657026363	-0.347253840526	0.407613042588	3.55220094953	0.459327602494	1.10979639921	0.0874934512843	-0.151512870502	0.0227864856808	1.00261908993	0.0492519297336	-0.510903138442	0.217119184841	0.0159288966468	-0.0728281307436	0.583886382672	-0.0731818950443	-0.0947831472408	0.352697610716	-0.0374870869394	0.366907808539	-17.3964705445	-17.6997203975	6.18739895537
101	2.83176978533	1.30107824822	-0.828406238589	4.41915994683	-1.16527848021	2.47748833353	-0.0941351812311	-0.0635128472087	0.0168532075736	-0.612808425468	0.121561143354	0.460773342371	0.118469806545	0.146132892744	-0.0330925018918	0.388138021211	0.025156569261	-0.121808542294	0.303234009435	0.0172972353683	0.371181571425	-43.087049374	-27.0702171806	-26.7638944376
102	4.54590032079	0.639056399339	-0.0523745734874	4.59972276507	-0.22744975376	3.67421419314	-0.0614159306733	-0.0393390246712	-0.0323408507797	-0.522216329123	0.0390499350323	-0.0626341966025	0.243267257851	0.180489242551	0.0151825614891	0.395854222206	0.07197228654	-0.0509819597184	0.297917512952	0.0281828106813	0.402872950967	-37.704675965	-36.5430746084	-24.1889043645
103	5.28472654786	0.111999049075	1.17467948515	8.40998758542	-4.19909738698	9.34326699347	-0.291047942787	0.878123174573	-0.363425914117	-1.5890772418	-0.227310089255	-0.0739486060769	0.914976218735	1.18708178676	0.585793423934	1.13508840509	0.0417024108199	-0.205716238178	0.557258087497	-0.036290617655	0.580112369947	-42.9378999089	-42.3419194905	-38.2249517902
104	1.86987758993	-1.09343965225	0.487020705402	0.623635518109	-0.357256407107	1.53014988293	0.0491057430712	0.10728234544	-0.0661693275626	-0.583834282061	0.127137337804	1.17577171324	0.208078559864	-0.432162037565	-0.255502848279	0.519041102659	-0.00701563825187	-0.354665118587	0.470646096509	0.121818684029	0.932637496508	-61.3899029319	-25.9681913441	-30.9140670982
105	1.20029563158	0.6268373886	0.307497342107	3.11605341909	-0.0381111260975	1.32793946902	0.01081890483	0.0515554264694	0.0758428672043	-0.500551926526	0.0822689680734	0.581687829895	0.0191000472277	-0.022008888013	-0.0518826997129	0.336859946606	0.0274277566306	-0.0527041848109	0.308083866635	0.0295036411283	0.377996247763	-40.711472057	-16.1299465418	-24.6842865548
106	4.34192206313	-0.951180379578	-0.401664759237	5.69563815263	-0.694134653265	3.6535381774	-0.195857547722	0.961350477301	0.297125319119	-1.09635917961	0.289584150447	-0.0530202908606	-0.143519859102	0.294268407871	-0.115191588137	0.824998961006	-0.122364219554	0.0289025327656	0.535508194474	0.00570874331093	0.281807418047	-29.6190526186	-4.56315770482	-38.2450761604

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 6 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 96 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 97 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 254 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 255 through 304 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 305 through 392 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 393 through 420 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 6 through 66 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 67 through 96 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 97 through 141 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 142 through 255 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 256 through 304 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 305 through 420 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 57 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 58 through 96 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 97 through 124 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 125 through 420 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 6 through 57 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 58 through 95 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 96 through 124 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 125 through 392 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 393 through 420 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 6 through 66 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 67 through 96 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 97 through 124 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 125 through 254 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 255 through 304 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 305 through 392 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 393 through 420 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 6 through 66 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 67 through 96 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 97 through 124 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 125 through 254 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 255 through 304 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 305 through 392 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 393 through 420 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 6 through 57 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 58 through 96 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 97 through 141 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 142 through 420 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 6 through 66 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 67 through 96 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 97 through 141 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 142 through 392 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 393 through 420 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 6 through 57 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 58 through 96 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 97 through 141 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 142 through 208 )
50	X-RAY DIFFRACTION	50	chain 'I' and (resid 209 through 304 )
51	X-RAY DIFFRACTION	51	chain 'I' and (resid 305 through 392 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 393 through 420 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 6 through 57 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 58 through 96 )
55	X-RAY DIFFRACTION	55	chain 'J' and (resid 97 through 124 )
56	X-RAY DIFFRACTION	56	chain 'J' and (resid 125 through 392 )
57	X-RAY DIFFRACTION	57	chain 'J' and (resid 393 through 420 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 6 through 57 )
59	X-RAY DIFFRACTION	59	chain 'K' and (resid 58 through 96 )
60	X-RAY DIFFRACTION	60	chain 'K' and (resid 97 through 124 )
61	X-RAY DIFFRACTION	61	chain 'K' and (resid 125 through 208 )
62	X-RAY DIFFRACTION	62	chain 'K' and (resid 209 through 420 )
63	X-RAY DIFFRACTION	63	chain 'L' and (resid 6 through 66 )
64	X-RAY DIFFRACTION	64	chain 'L' and (resid 67 through 96 )
65	X-RAY DIFFRACTION	65	chain 'L' and (resid 97 through 124 )
66	X-RAY DIFFRACTION	66	chain 'L' and (resid 125 through 304 )
67	X-RAY DIFFRACTION	67	chain 'L' and (resid 305 through 420 )
68	X-RAY DIFFRACTION	68	chain 'M' and (resid 6 through 96 )
69	X-RAY DIFFRACTION	69	chain 'M' and (resid 97 through 141 )
70	X-RAY DIFFRACTION	70	chain 'M' and (resid 142 through 420 )
71	X-RAY DIFFRACTION	71	chain 'N' and (resid 6 through 57 )
72	X-RAY DIFFRACTION	72	chain 'N' and (resid 58 through 96 )
73	X-RAY DIFFRACTION	73	chain 'N' and (resid 97 through 124 )
74	X-RAY DIFFRACTION	74	chain 'N' and (resid 125 through 254 )
75	X-RAY DIFFRACTION	75	chain 'N' and (resid 255 through 420 )
76	X-RAY DIFFRACTION	76	chain 'O' and (resid 6 through 66 )
77	X-RAY DIFFRACTION	77	chain 'O' and (resid 67 through 96 )
78	X-RAY DIFFRACTION	78	chain 'O' and (resid 97 through 124 )
79	X-RAY DIFFRACTION	79	chain 'O' and (resid 125 through 392 )
80	X-RAY DIFFRACTION	80	chain 'O' and (resid 393 through 420 )
81	X-RAY DIFFRACTION	81	chain 'P' and (resid 6 through 57 )
82	X-RAY DIFFRACTION	82	chain 'P' and (resid 58 through 96 )
83	X-RAY DIFFRACTION	83	chain 'P' and (resid 97 through 124 )
84	X-RAY DIFFRACTION	84	chain 'P' and (resid 125 through 208 )
85	X-RAY DIFFRACTION	85	chain 'P' and (resid 209 through 255 )
86	X-RAY DIFFRACTION	86	chain 'P' and (resid 256 through 392 )
87	X-RAY DIFFRACTION	87	chain 'P' and (resid 393 through 420 )
88	X-RAY DIFFRACTION	88	chain 'Q' and (resid 6 through 57 )
89	X-RAY DIFFRACTION	89	chain 'Q' and (resid 58 through 124 )
90	X-RAY DIFFRACTION	90	chain 'Q' and (resid 125 through 420 )
91	X-RAY DIFFRACTION	91	chain 'R' and (resid 6 through 57 )
92	X-RAY DIFFRACTION	92	chain 'R' and (resid 58 through 96 )
93	X-RAY DIFFRACTION	93	chain 'R' and (resid 97 through 141 )
94	X-RAY DIFFRACTION	94	chain 'R' and (resid 142 through 255 )
95	X-RAY DIFFRACTION	95	chain 'R' and (resid 256 through 370 )
96	X-RAY DIFFRACTION	96	chain 'R' and (resid 371 through 420 )
97	X-RAY DIFFRACTION	97	chain 'W' and (resid 6 through 57 )
98	X-RAY DIFFRACTION	98	chain 'W' and (resid 58 through 96 )
99	X-RAY DIFFRACTION	99	chain 'W' and (resid 97 through 141 )
100	X-RAY DIFFRACTION	100	chain 'W' and (resid 142 through 420 )
101	X-RAY DIFFRACTION	101	chain 'T' and (resid 6 through 57 )
102	X-RAY DIFFRACTION	102	chain 'T' and (resid 58 through 96 )
103	X-RAY DIFFRACTION	103	chain 'T' and (resid 97 through 124 )
104	X-RAY DIFFRACTION	104	chain 'T' and (resid 125 through 208 )
105	X-RAY DIFFRACTION	105	chain 'T' and (resid 209 through 392 )
106	X-RAY DIFFRACTION	106	chain 'T' and (resid 393 through 420 )

+
万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

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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

-
構造ビューア

+
ビューアのログ

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このページ

-
このウェブサイト

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オプション

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データを開く

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基本情報

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構造の表示

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ダウンロードとリンク

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ダウンロード

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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)