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万見

- PDB-6pxa: The crystal structure of chloramphenicol acetyltransferase-like p... -

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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: 6pxa

タイトル

The crystal structure of chloramphenicol acetyltransferase-like protein from Vibrio fischeri ES114 in complex with taurocholic acid

要素

Chloramphenicol acetyltransferase

キーワード

TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

機能・相同性

機能・相同性情報

chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic / metal ion binding
類似検索 - 分子機能

生物種

Aliivibrio fischeri (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: 1.82 Å

データ登録者

Tan, K. / Maltseva, N. / Jedrzejczak, R. / Kuhn, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

資金援助

米国, 1件

引用

ジャーナル: Microbiol Resour Announc / 年: 2025
タイトル: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
著者: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...

履歴

登録	2019年7月25日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2019年9月25日	Provider: repository / タイプ: Initial release
改定 1.1	2019年12月18日	Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.2	2023年10月11日	Group: Data collection / Database references / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.3	2025年6月18日	Group: Database references / Structure summary カテゴリ: citation / citation_author / pdbx_entry_details Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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	6pxa.cif.gz	1.3 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6pxa.ent.gz	895.3 KB	表示	PDB形式
PDBx/mmJSON形式	6pxa.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	6pxa_validation.pdf.gz	3.2 MB	表示	wwPDB検証レポート
文書・詳細版	6pxa_full_validation.pdf.gz	3.3 MB	表示
XML形式データ	6pxa_validation.xml.gz	106 KB	表示
CIF形式データ	6pxa_validation.cif.gz	139.6 KB	表示
アーカイブディレクトリ	https://data.pdbj.org/pub/pdb/validation_reports/px/6pxa ftp://data.pdbj.org/pub/pdb/validation_reports/px/6pxa	HTTPS FTP

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関連構造データ

関連構造データ	5umeC 5uswC 5usxC 5utxC 5uu6C 5uwyC 5ux9SC 5wp0C 6aonC 6aooC 6aziC 6b5fC 6b8dC 6bk7C 6blbC 6c8qC 6pu9C 6puaC 6w2zC 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	5ux9-1 6pub-1 5ux9-2 6iz4-3 3a73-1 6iz1-1 3wks-d 6rko-d Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) 類似検索 - 機能・相同性F&H 検索類似検索 - 機能F&H 検索類似検索 - 相同性F&H 検索
その他のデータベース	TargetTrack: CSGID-IDP07301

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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	#39 - 2003年3月 lac転写抑制因子 (lac Repressor) 類似性 (5) #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 (3) #49 - 2004年1月炭酸脱水酵素 (Carbonic Anhydrase) 類似性 (3)

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集合体

登録構造単位

A: Chloramphenicol acetyltransferase

B: Chloramphenicol acetyltransferase

C: Chloramphenicol acetyltransferase

D: Chloramphenicol acetyltransferase

E: Chloramphenicol acetyltransferase

F: Chloramphenicol acetyltransferase

G: Chloramphenicol acetyltransferase

H: Chloramphenicol acetyltransferase

I: Chloramphenicol acetyltransferase

J: Chloramphenicol acetyltransferase

K: Chloramphenicol acetyltransferase

L: Chloramphenicol acetyltransferase

ヘテロ分子

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

A: Chloramphenicol acetyltransferase

B: Chloramphenicol acetyltransferase

C: Chloramphenicol acetyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
76.3 kDa, 3 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

D: Chloramphenicol acetyltransferase

E: Chloramphenicol acetyltransferase

F: Chloramphenicol acetyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
76.2 kDa, 3 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

G: Chloramphenicol acetyltransferase

H: Chloramphenicol acetyltransferase

I: Chloramphenicol acetyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
76.3 kDa, 3 ポリマー
Omokage検索でこの集合体の類似形状データを探す (詳細)

J: Chloramphenicol acetyltransferase

K: Chloramphenicol acetyltransferase

L: Chloramphenicol acetyltransferase

ヘテロ分子

登録者・ソフトウェアが定義した集合体
76.5 kDa, 3 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)	43.519, 121.363, 146.170
Angle α, β, γ (deg.)	89.399, 89.911, 87.602
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

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タンパク質 , 1種, 12分子 ABCDEFGHIJKL

#1: タンパク質	Chloramphenicol acetyltransferase 分子量: 24745.918 Da / 分子数: 12 / 由来タイプ: 組換発現由来: (組換発現) Aliivibrio fischeri (strain ATCC 700601 / ES114) (バクテリア) 株: ATCC 700601 / ES114 / 遺伝子: VF_A0790 / プラスミド: pMCSG53 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): -Magic 参照: UniProt: Q5DZD6, chloramphenicol O-acetyltransferase

#1: タンパク質

Chloramphenicol acetyltransferase

分子量: 24745.918 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現)

Aliivibrio fischeri (strain ATCC 700601 / ES114) (バクテリア)
株: ATCC 700601 / ES114 / 遺伝子: VF_A0790 / プラスミド: pMCSG53 / 発現宿主:

Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): -Magic
参照: UniProt: Q5DZD6, chloramphenicol O-acetyltransferase

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非ポリマー , 7種, 825分子

#2: 化合物	ChemComp-TCH / TAUROCHOLIC ACID / タウロコ-ル酸分子量: 515.703 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C₂₆H₄₅NO₇S / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物	ChemComp-CL / CHLORIDE ION / クロリド分子量: 35.453 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Cl
#4: 化合物	ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 天然 / 式: SO₄
#5: 化合物	ChemComp-ACT / ACETATE ION / 酢酸イオン分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C₂H₃O₂
#6: 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: 7 / 由来タイプ: 合成 / 式: C₃H₈O₃
#7: 化合物	ChemComp-FMT / FORMIC ACID / ギ酸分子量: 46.025 Da / 分子数: 7 / 由来タイプ: 合成 / 式: CH₂O₂
#8: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 776 / 由来タイプ: 天然 / 式: H₂O

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詳細

研究の焦点であるリガンドがあるか	Y
Has protein modification	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: 2.62 Å³/Da / 溶媒含有率: 53.12 %
結晶化	温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 / 詳細: 0.2 M Sodium acetate, 0.1 M Tris, 16% (w/v) PEG4000

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データ収集

回折	平均測定温度: 100 K / Serial crystal experiment: N
放射光源	由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.9789 Å
検出器	タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年3月19日 / 詳細: mirror
放射	モノクロメーター: Si 111 / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長	波長: 0.9789 Å / 相対比: 1
反射	解像度: 1.82→46.9 Å / Num. obs: 257772 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / 冗長度: 3.4 % / B_iso Wilson estimate: 33.74 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.053 / R_rim(I) all: 0.1 / Χ²: 2.052 / Net I/σ(I): 25.3
反射シェル	解像度: 1.82→1.84 Å / 冗長度: 3.2 % / R_merge(I) obs: 0.718 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9761 / CC_1/2: 0.783 / R_pim(I) all: 0.447 / R_rim(I) all: 0.85 / Χ²: 0.829 / % possible all: 92

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解析

ソフトウェア

名称	バージョン	分類
SBC-Collect		データ収集
PHENIX	1.15.2_3472	精密化
HKL-3000		データ削減
HKL-3000		データスケーリング
HKL-3000		位相決定

精密化

構造決定の手法:

分子置換
開始モデル: 5UX9

5ux9

解像度: 1.82→46.9 Å / SU ML: 0.2505 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 30.7683

	R_factor	反射数	%反射	Selection details
R_free	0.2377	12605	4.9 %	random
R_work	0.1974	-	-	-
obs	0.1993	257109	95.97 %	-

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: 50.99 Å²

精密化ステップ

サイクル: LAST / 解像度: 1.82→46.9 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	20682	0	531	776	21989

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0089	21805
X-RAY DIFFRACTION	f_angle_d	1.0062	29595
X-RAY DIFFRACTION	f_chiral_restr	0.0639	3147
X-RAY DIFFRACTION	f_plane_restr	0.006	3745
X-RAY DIFFRACTION	f_dihedral_angle_d	16.2916	12372

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 (%)
1.82-1.84	0.4246	336	0.3668	7250	X-RAY DIFFRACTION	85.68
1.84-1.86	0.3666	396	0.3477	7935	X-RAY DIFFRACTION	93.85
1.86-1.89	0.3591	405	0.332	8238	X-RAY DIFFRACTION	95.78
1.89-1.91	0.3336	421	0.3	8131	X-RAY DIFFRACTION	95.67
1.91-1.93	0.368	379	0.2986	7768	X-RAY DIFFRACTION	92.16
1.93-1.96	0.3294	429	0.2835	8292	X-RAY DIFFRACTION	96.91
1.96-1.99	0.284	443	0.2665	8352	X-RAY DIFFRACTION	97.85
1.99-2.02	0.324	448	0.2668	8199	X-RAY DIFFRACTION	97.96
2.02-2.05	0.3075	438	0.2573	8338	X-RAY DIFFRACTION	97.77
2.05-2.08	0.2905	474	0.2549	8287	X-RAY DIFFRACTION	97.81
2.08-2.12	0.3017	409	0.2439	8323	X-RAY DIFFRACTION	97.76
2.12-2.16	0.2792	439	0.2348	8259	X-RAY DIFFRACTION	97.71
2.16-2.2	0.2914	454	0.2343	8243	X-RAY DIFFRACTION	97.73
2.2-2.24	0.2981	435	0.2278	8312	X-RAY DIFFRACTION	97.45
2.24-2.29	0.2895	436	0.2202	8331	X-RAY DIFFRACTION	97.34
2.29-2.35	0.2529	411	0.213	7832	X-RAY DIFFRACTION	93.82
2.35-2.4	0.2761	397	0.2203	8429	X-RAY DIFFRACTION	97.95
2.4-2.47	0.2811	419	0.2163	8285	X-RAY DIFFRACTION	98.02
2.47-2.54	0.296	415	0.2179	8406	X-RAY DIFFRACTION	97.88
2.54-2.62	0.2585	413	0.2056	8264	X-RAY DIFFRACTION	98.06
2.62-2.72	0.2516	442	0.2028	8440	X-RAY DIFFRACTION	98.22
2.72-2.83	0.2574	464	0.2034	8226	X-RAY DIFFRACTION	98.5
2.83-2.96	0.2398	445	0.1998	8310	X-RAY DIFFRACTION	97.77
2.96-3.11	0.2611	405	0.2099	8174	X-RAY DIFFRACTION	94.82
3.11-3.31	0.2258	372	0.2008	8308	X-RAY DIFFRACTION	98.3
3.31-3.56	0.2201	513	0.1905	8214	X-RAY DIFFRACTION	97.63
3.56-3.92	0.2153	419	0.1753	8175	X-RAY DIFFRACTION	96.05
3.92-4.49	0.1902	324	0.1542	7359	X-RAY DIFFRACTION	86.29
4.49-5.65	0.1786	429	0.1473	7647	X-RAY DIFFRACTION	90.52
5.65-46.9	0.1835	395	0.1658	8177	X-RAY DIFFRACTION	95.84

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	1.5520026152	0.0970496786316	1.26761364337	3.7950289254	0.528461578309	8.13477666351	-0.0829866020385	-0.10608448165	0.382889876286	-0.065010456195	-0.029550160272	0.433069361521	-0.3953991574	-0.673445003919	0.127765483264	0.495923008953	0.0565249655222	-0.0519133636509	0.341241312939	0.0704655639524	0.433370473378	-11.5043407155	16.9539591614	-4.57703726169
2	8.89704644228	2.5069749189	-1.78313101409	2.88368812098	-2.95260459579	4.25158768862	0.219760640405	-0.998791470376	0.618364760629	0.818080684673	-0.0389514629457	0.305231207351	-0.571601220494	-0.396890032159	-0.204760659573	0.622690504948	0.0929835432998	0.0379100256102	0.423709650888	-0.0343298280742	0.475197577855	-9.7777865652	16.7264822328	11.6530239829
3	0.988810303394	-0.253799762932	1.25191693915	2.55608506901	-1.33701583058	6.17462721537	-0.0460888943713	-0.143181354705	0.193907282892	0.394486940927	-0.0332827768497	0.0776782829194	-0.268270570166	-0.15177191525	0.101480360124	0.499524368993	-0.0242907781197	-0.023023197071	0.319061857376	0.0163265028613	0.297354934135	1.11226019001	12.5850732262	11.501566189
4	1.62895504741	0.222778438496	-0.245497303516	3.42718460544	-1.80782166307	2.97693157308	-0.0372492618139	0.00943174740792	0.120777583002	0.00474596249931	-0.0612545315705	-0.218464003174	-0.208601640572	0.0666659305902	0.0977157751732	0.546013164218	-0.0409452652529	-0.039985422683	0.285620096844	0.0409657579015	0.319527826841	8.27701150521	23.7016515906	-12.2447032591
5	6.05211004518	0.386597861751	-2.22835718957	2.20524061884	-1.74756898373	3.96761720215	0.365186465597	0.135303672344	-0.147089776414	0.0329547911249	0.040944087556	1.51270405223	0.406519529467	-0.67475059402	-0.298005565793	0.608411100265	0.00101174079642	-0.034126887751	0.374223107679	0.00273258906147	0.429453629803	-14.6310940425	0.44949401447	16.2447717078
6	1.18935921465	0.863201602274	-0.279574769911	2.82481463219	2.15781722972	2.60207896674	0.108902404664	-0.0658341394374	-0.0602962707605	0.776946566118	0.0869728939742	0.365939373653	0.112508339306	-0.00666730371762	-0.273775965492	0.342794481648	-0.0124177732848	-0.0244194558318	0.351654658272	0.0655849972056	0.362044255122	-8.91869111775	-6.1691788208	15.5031238565
7	6.25960734504	3.24155050873	-1.92725926327	6.78703231394	-2.08780494725	6.23052182343	-0.151302580044	-0.248161848892	-0.388692668946	-0.295799832705	-0.00774819277032	1.47381973151	0.512615960397	-0.858177062022	0.131474395578	0.351433623207	-0.016812686594	0.0320648054634	0.450719210417	0.0697065094716	0.632073424322	-13.1705734675	-19.2096369683	9.21020514608
8	3.15855169259	0.292743309079	0.13614760476	6.49941011763	2.40491550121	3.59121253309	0.118276327441	-0.0941288764258	-0.443827985114	0.735844024882	-0.21807341225	-0.0248674997066	0.612456343294	-0.153774623893	0.0502041960243	0.64785202166	-0.0142974859523	0.0191131146232	0.294470274264	0.0821894760694	0.308738128221	-3.30194927081	-17.4828088773	16.0149854588
9	0.691671388552	0.182864513849	0.35807478187	3.08769866625	1.5295081081	3.21450456671	-0.0229032371721	-0.0990422789391	-0.0395248157608	0.319358318546	-0.0254502250668	0.090871228788	0.213971286253	-0.0149469032869	0.033668360006	0.28523639285	0.00704312768341	-0.0386738959922	0.272161607652	0.0693503952025	0.32604823458	2.05569185071	-13.9930486101	5.48199335566
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46	2.08156468499	-0.130169125392	-1.47286451661	6.86625809194	2.09803077523	3.62974117169	-0.0242681227984	0.610967910396	-0.528575435625	-1.29026864401	-0.0652550397514	0.231207671896	0.812049431293	0.0803784688014	0.0326256046611	0.949961625905	0.0388904372432	-0.0188764505829	0.324130178763	-0.0039769345065	0.290196837138	9.54835315251	-33.8118795641	-95.9801283671
47	5.35781807339	-0.214112859045	-3.36905066537	4.79922943109	1.79658573049	6.99453372744	-0.217869314336	-0.0575361288548	0.0661960110446	-0.0860006215923	0.0506061126909	-0.757092267167	0.44933515997	0.658569650979	0.143878133856	0.433662879543	-0.027226083901	0.0581822096791	0.331979904861	0.0496362715876	0.452768047701	34.1136423648	-47.433694021	-39.667268762
48	6.96035945514	-1.30524883669	1.76221432326	8.35207445611	2.98447832714	8.67741855639	-0.139060745435	0.519042545383	0.861199725126	-1.12777802534	-0.142577461539	-1.2607150073	-0.341957435328	0.555547817637	0.309500891857	0.714445869614	0.00575572387812	0.140922270921	0.34838364461	0.073009581361	0.506165804338	29.3153897896	-52.2305233161	-55.3027752649
49	1.14122651066	0.00730113274751	1.25024145401	2.78395147883	-0.133628515472	2.5430916556	-0.00525786219378	0.245921607856	0.0567065282285	-0.402708373447	0.0572531393519	-0.357227307967	-0.154828626905	0.155232328587	-0.0392832300525	0.499754799944	-0.00252574713884	0.102035482046	0.285845126697	0.0507215562907	0.320370116276	27.5076258235	-55.4966883623	-46.4518157476
50	8.21787662296	-3.8186537333	-0.983725052345	4.51530871252	2.07481277582	4.01359698825	0.227659538055	1.78479347197	-0.789012630696	-0.671712425869	-0.496059703881	-0.390797570252	0.800731831271	0.505666007833	0.239403042598	1.23138937847	0.142801416557	0.196619529734	0.549745751586	-0.0400168432216	0.608923030453	30.0828632222	-66.8439169777	-60.9310428833
51	0.24649181342	0.828042075282	0.226426504116	6.10601060895	1.25841435251	1.21585380829	0.046334017023	0.10892277847	-0.102565668772	-0.46304208737	0.0150805824004	-0.446561024406	0.068275465904	0.0344613060036	-0.0551518457713	0.580016786903	0.0583885091388	0.0108605488455	0.261690350993	-0.0210058226986	0.301720335327	18.7830718819	-68.3885736972	-51.9169417065
52	0.373690366789	0.466742901137	0.65069808169	5.75050284906	1.21585932046	1.12136042079	-0.0195879643178	0.122469396235	-0.0284600542276	-0.55557852691	-0.10675977633	-0.10269860792	-0.146540855961	-0.0137435792998	0.0379311450667	0.674386500617	-0.00403251268499	0.0230236386644	0.292509670661	-0.0175653491461	0.254950431096	16.7088406646	-62.2410624137	-52.9905682024
53	3.8738161875	-1.23066686922	0.885011260205	8.59944178691	-1.02558775484	2.34837614202	-0.0738638235554	0.140979056011	-0.168483665215	-0.227140738049	0.150483731257	0.23940166894	0.0397763754355	-0.336484259708	-0.0664406312668	0.543483202007	-0.0203469797473	0.00332600356215	0.226551806559	0.0167100034713	0.19978227759	9.24258546179	-52.0839474122	-48.0431259549
54	2.26373497109	1.3437454927	-1.31985730212	4.46401636282	-5.91961081366	8.07753509956	0.0535177301021	0.284218115147	0.0563454660673	-1.07360500157	0.0608917522008	0.33919182104	0.238080164663	-0.0876729717877	-0.188898995978	0.494444981224	0.0311075748009	-0.00920510512417	0.2326131841	-0.00305673261273	0.258673328555	3.64693008456	-42.9045137005	-50.6394620468
55	6.88596484699	2.16042764761	-2.47486008335	2.2201273584	-2.93409803164	4.78441271213	0.163006831625	0.422718141937	0.399281698033	-0.237019575807	0.148862256224	-0.0603557252253	0.050064270388	-0.235851496005	-0.278806792889	0.687184422668	0.0529292098217	0.0108628399898	0.267723969866	0.0797894789004	0.30240719894	16.9154840949	-31.2680821663	-54.0731597512
56	8.81620308224	4.11610687703	-3.28403433599	4.6108242401	-5.68391469789	7.6253371957	-0.195253414086	0.350061308907	0.45794245125	-0.649270706738	0.117105996426	-0.0498565087244	0.473453726723	-0.188133073053	0.119383026998	0.847664404147	0.0378608167197	0.0132509248005	0.25522723015	0.0331845491021	0.305703246223	9.73839689386	-27.0306632079	-58.445961244
57	1.49962083193	0.63319665643	-0.179227811584	3.52550611568	-1.27580815376	5.115505832	0.119920892736	-0.0157874800291	-0.372295633662	-0.265255188809	-0.196732654043	-0.668602942289	0.366807320167	0.310725071729	5.4689245892E-5	0.503740657702	0.0557677796958	-0.0449967417101	0.274439566035	-0.0153653435385	0.37608123397	26.5510065791	-77.8046658191	-38.7450261916
58	6.1805176094	3.83285215454	-0.85947870793	7.90202060799	-1.60811432828	5.51732365767	0.404607227207	-1.17535044986	-0.625769724435	1.10910875345	-0.359070526773	-0.691333754698	0.5935247049	0.292643230696	0.177632514039	0.806558223355	0.0169176107639	-0.127627078139	0.41444422468	0.067437921844	0.475587621394	23.9047420283	-79.4698098702	-20.1961664557
59	0.72176631264	-0.216836811583	0.439850570203	1.36368359899	0.22435681659	2.31525394378	-0.0142027676174	-0.143432711646	-0.120654976249	0.300219615849	-0.038511576959	-0.117452514747	0.0961358223084	0.0130870848255	0.0285809542208	0.669639354326	-0.0152217417283	-0.0302256089168	0.277038788395	0.041050396689	0.287417067892	13.3488917325	-73.8016023137	-26.2541322008
60	1.62452533119	-0.755108743101	-0.411762597059	7.21989411593	2.66367805845	2.69990972481	0.0296350698576	0.0567170107978	-0.323243792195	-0.252121658709	-0.0200133646889	0.140254879683	0.322562591397	-0.0598673131375	0.0153903471298	0.581319028388	-0.0119991007347	-0.0692674107667	0.237142079738	0.00478753887899	0.268627825975	7.22563788235	-84.8349743526	-47.8604688458
61	2.13016907751	-3.22295048622	-2.0311305071	7.99273531317	5.19148544992	3.46156603169	-0.419964937531	0.377263813767	-0.953852010194	-0.369872671265	0.449121386772	0.135217774324	0.332966465925	-0.200457379534	0.0669342452428	0.678310179998	-0.0556969666189	-0.0125394625224	0.380836537485	-0.110237961441	0.469676966206	6.23012770631	-96.9429414598	-55.3252247861
62	1.52117288647	-1.13624679508	0.314171195436	6.41787343169	0.413222227931	3.19567038439	0.0159050693807	-0.0195949176538	0.0776363223216	0.396224820595	0.138233147254	-1.17807556969	0.0898955353185	0.546954507607	-0.115404701739	0.467785014092	-0.0440113544954	-0.139380624682	0.422078958634	0.0279625595205	0.513084541581	29.2138513826	-58.634950581	-19.2309263539
63	1.76331499974	-0.525232026843	0.317176935832	5.71327394884	-3.48957837386	4.4629781326	0.0868532040147	-0.20804823775	0.162063321596	0.223104293368	-0.141605715442	-0.495992662419	-0.0718993386322	0.196579963721	0.0521590190604	0.495716548373	-0.0387247656886	-0.0815349035535	0.273542682987	-0.0243276389688	0.295747479175	24.3886505296	-53.8015916126	-22.5359112533
64	1.97547576633	-2.29844170778	0.787284263004	7.48345860162	-0.209581780389	4.15886196169	-0.146800407033	-0.211180038469	1.51421875812	0.139609564043	-0.14669912313	-1.37971560987	-0.37883099867	1.03110313622	0.254235162075	0.792963066765	-0.148696268636	-0.00901875623695	0.5422901165	0.02487379064	0.893665685394	26.9968923089	-36.0877188902	-24.926257256
65	0.563480164498	-0.0196145559435	-0.6927457866	2.83085122097	-2.84013222142	5.27774814836	0.0485428039774	-0.152346760162	0.169940529529	0.256298800012	-0.0469862339017	-0.178583616717	-0.300712066128	0.137741413492	0.00606820327866	0.532576639526	-0.0253536771752	-0.0139969379156	0.230547527286	-0.0167866169507	0.274081099475	17.7204328688	-43.7258145409	-33.5142703234
66	5.13486897842	3.92807503246	-4.32238292493	7.03863754762	-5.38077491088	4.70603579487	0.0831989337075	0.0227263006585	0.55475048268	0.573765604124	0.0873483718222	0.0351226407206	-0.782169731121	-0.10181890278	-0.164355223557	0.665797329802	-0.00446958375956	-0.0323553386251	0.300279350359	-0.00386634039789	0.395272696152	17.2996809154	-33.2185628909	-35.6155186237
67	2.65758280955	0.935288892813	-0.483220324544	2.6913354948	0.177810649752	1.50007686123	0.0990109821551	-0.221864840237	0.0398454110525	0.311324008306	-0.0219421787537	0.0519750866728	-0.203233724539	-0.0911977819451	-0.0490193126009	0.622467261022	0.0101809137878	-0.0140702857618	0.259064087637	0.00775229729056	0.226016107388	8.83009093422	-55.3213764851	-23.1331157351
68	3.23464553266	-0.843752296905	-1.348236368	3.35032743455	0.753589069958	8.65740875055	0.142820162986	0.15416973357	-0.158862270948	-0.500069998775	0.0324308476416	0.310695952986	0.0413447440316	-0.80035438869	-0.113551176027	0.549830065852	-0.0269051399473	0.00798707334572	0.256721396556	0.0310782950216	0.304852269498	-0.0716076696616	-60.4737162738	-22.1496086041
69	2.36879264778	0.948333755609	1.26466322349	2.09735250139	0.718972104872	6.91232056727	0.11297683907	-0.626650309939	0.0634598993256	1.02100621828	-0.123245418984	0.150667722601	-0.134540035602	-0.242548998917	0.0203114575496	1.00503855509	0.0221381446699	0.0561250480098	0.524899010786	-0.0278026353639	0.282760264901	5.83628892003	-58.9394473102	-3.25058063978
70	4.77283622072	-1.42260469972	0.817500763241	2.45905220425	1.04029551125	1.96839295306	0.00250303532966	-0.724199588992	0.0744462013421	1.32138268232	-0.100345413328	0.215667754753	-0.416602583634	-0.94711011334	0.0887504224563	0.987511478208	0.0560499240442	0.0993179919591	0.790227700099	0.0269783748085	0.30005040177	1.09327300593	-58.4252092411	3.18057022561
71	1.74208898892	-0.395660009191	0.235835071542	4.94709423456	0.0573510735876	7.85739403954	-0.0668061024379	0.238914902163	-0.0146285745388	-0.307052600766	0.034025676641	-0.483333646461	0.0918640533972	0.610854287687	0.00724443946226	0.281868319782	-0.0123438521955	0.00184582402258	0.306787755869	0.0375752480803	0.383488989201	28.9631357952	-49.6077073623	25.1506093878
72	5.90658352767	-0.458695429115	1.01733435322	6.92977931052	-3.75135057428	4.86526471066	0.576873830009	0.747642980895	-0.735358551908	-0.927061911296	-0.312820921563	-0.811092529886	0.365290488396	0.662359272186	-0.217740396935	0.568131993984	0.0671258438862	-0.0404497781762	0.418418831169	-0.131928715252	0.48863434228	26.8227927076	-65.4592620109	15.2138061334
73	0.423932509837	0.514726793392	-0.140244228216	4.67314088908	-0.368090788668	0.784697075034	-0.0586306316331	0.201975619635	-0.132122104562	-0.718526324234	-0.0116990352953	0.013201290914	0.0590162842096	-0.00104730192757	0.0970669869491	0.438435835114	-0.000836800826425	-0.0432850292031	0.295736290171	-0.0475922443434	0.295899660579	16.3246223568	-65.2311835141	21.2494999162
74	0.680311958102	-0.228354483835	0.134936145469	5.41836943771	-2.30801748055	2.41832216297	0.0326569649447	0.187595842391	0.0554047849871	-0.0703318155112	0.0393573183839	0.247820732477	-0.295416295364	-0.0112761145049	-0.0939820696006	0.38058871535	0.00755710479262	-0.0583351820887	0.310057570732	0.0347925681159	0.266312583425	9.19831639046	-38.7174772663	20.6935016017
75	7.1287636373	1.10767590809	-1.82028394741	0.970387378499	-2.31479578055	5.40152873063	-0.0586380858982	-0.158523394008	-0.428420740522	-0.442524477849	-0.442226157832	-1.26097740712	0.574346733095	0.667058463084	0.525113124262	0.447122968214	0.057225878163	-0.0310470174617	0.331454913957	-0.0122191832028	0.60262572121	31.2193687658	-74.417961828	30.5755734096
76	1.80012580251	1.2196504891	-1.19382232471	3.10530963537	1.2594541078	4.40135627643	0.0482614218288	-0.203169838945	-0.389078445278	0.529599334195	-0.243444853014	-0.641222050161	0.996555094032	0.749829631302	-0.0793594916192	-0.0784627178454	0.0359261806404	-0.081769438477	0.355374570776	-0.0454935483155	0.568892410511	25.2134230797	-76.5029250301	36.9845667562
77	2.79571682637	-2.51223480429	0.488921628707	3.5461359538	-2.52429367432	5.35119141164	-0.126183505555	0.0751963119435	-0.454885191851	1.52462289419	-0.0568656612128	-1.55143746375	0.402957666858	1.265574273	0.0871387675795	0.767296949011	0.0450860615214	-0.268563737451	0.439082891704	0.0879337011983	0.724735915434	28.2031671141	-75.7849945271	51.3083244879
78	1.2304080187	0.0719574617797	-0.480627905954	1.01743071847	0.913023807286	3.35460413833	-0.00897547174971	-0.241616365035	-0.369311933859	0.919357266438	0.0235447120214	-0.126066790639	0.477473733821	0.343436111514	-0.0996357673214	0.733444228394	-0.019465337193	-0.0690308042206	0.294330889232	0.0610670823729	0.430101075878	16.9883793742	-74.4985707072	49.1655984403
79	0.939433047536	0.0857753397485	0.977065440499	1.48525081925	0.153912520892	3.17892423392	0.0521900901532	-0.189433209475	-0.235989026233	0.721322999649	-0.0785394673062	-0.0481143322746	0.131654218731	-0.0161267494823	-0.0225308166823	0.543172643251	-0.0424402929887	-0.018165743002	0.264453908862	0.0435089942133	0.329695847473	12.9908787454	-71.3348048968	47.0549617877
80	2.07754999625	1.21613566851	0.196479958845	9.10459265	3.64243417399	3.89221278133	0.00282037850927	0.23545657175	-0.499824386625	-0.157338232593	-0.0116768640242	0.152556824615	0.675882381084	-0.291571749475	0.00418581521672	0.484549094723	-0.0709245306446	-0.0406547594869	0.345410062674	-0.0382289139958	0.449992205775	5.43723330952	-88.1009278407	25.6557722402
81	1.60313287315	1.05999398756	0.903515001381	2.61425415366	-1.6717640737	2.96446732679	0.0580629836415	-0.157996333715	-0.198262934169	0.902214106009	-0.280667338597	-0.890415117985	-0.273401647964	0.262109574538	0.15819221443	0.64646317507	-0.0447103131687	-0.169104001599	0.334638993069	0.0737359463208	0.46888128663	28.4713246833	-53.3080005355	51.1787831485
82	3.35409898677	2.1155142517	-2.9590601295	5.69528943714	1.77104926365	6.2578018097	0.184830786202	-0.27394246466	1.3300129551	0.581071192632	0.285946670171	-0.57035733458	-1.18539536679	0.561779496929	-0.475635702642	0.971320183392	-0.0993035077416	-0.125745862664	0.400532684399	0.0320531401595	0.647807301882	29.1907261024	-34.2649737215	45.5654681565
83	1.0556956855	0.255186956028	0.053994075093	1.76160894033	-0.384507442188	1.59198434762	0.0839073788402	-0.273512654316	0.0307360855024	0.94808426619	-0.0968651374914	0.172456610979	-0.348029513926	-0.103895220814	0.0293887995183	0.783567594401	-0.0148076703106	0.0266868901771	0.303610847298	-0.000326541579518	0.303900774476	12.582490722	-49.2835143094	53.5919883892

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 0 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 136 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 137 through 217 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -2 through 17 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 42 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 43 through 59 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 60 through 75 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 76 through 162 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 163 through 173 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 174 through 183 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 184 through 204 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 205 through 217 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 0 through 28 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 29 through 42 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 43 through 67 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 68 through 105 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 106 through 118 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 119 through 136 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 137 through 162 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 163 through 173 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 174 through 183 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 184 through 204 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 205 through 218 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 3 through 42 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 43 through 67 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 68 through 173 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 174 through 217 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid -2 through 21 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 22 through 35 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 36 through 53 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 54 through 67 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 68 through 105 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 106 through 118 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 119 through 162 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 163 through 183 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 184 through 204 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 205 through 218 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 2 through 12 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 13 through 24 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 25 through 42 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 43 through 59 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 60 through 75 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 76 through 136 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 137 through 204 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 205 through 218 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid -2 through 12 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 13 through 24 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 25 through 53 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 54 through 67 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 68 through 105 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 106 through 136 )
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 137 through 162 )
54	X-RAY DIFFRACTION	54	chain 'G' and (resid 163 through 183 )
55	X-RAY DIFFRACTION	55	chain 'G' and (resid 184 through 204 )
56	X-RAY DIFFRACTION	56	chain 'G' and (resid 205 through 217 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 3 through 42 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 43 through 67 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 68 through 151 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 152 through 204 )
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 205 through 218 )
62	X-RAY DIFFRACTION	62	chain 'I' and (resid -2 through 21 )
63	X-RAY DIFFRACTION	63	chain 'I' and (resid 22 through 53 )
64	X-RAY DIFFRACTION	64	chain 'I' and (resid 54 through 67 )
65	X-RAY DIFFRACTION	65	chain 'I' and (resid 68 through 105 )
66	X-RAY DIFFRACTION	66	chain 'I' and (resid 106 through 118 )
67	X-RAY DIFFRACTION	67	chain 'I' and (resid 119 through 162 )
68	X-RAY DIFFRACTION	68	chain 'I' and (resid 163 through 173 )
69	X-RAY DIFFRACTION	69	chain 'I' and (resid 174 through 204 )
70	X-RAY DIFFRACTION	70	chain 'I' and (resid 205 through 218 )
71	X-RAY DIFFRACTION	71	chain 'J' and (resid 0 through 42 )
72	X-RAY DIFFRACTION	72	chain 'J' and (resid 43 through 67 )
73	X-RAY DIFFRACTION	73	chain 'J' and (resid 68 through 136 )
74	X-RAY DIFFRACTION	74	chain 'J' and (resid 137 through 217 )
75	X-RAY DIFFRACTION	75	chain 'K' and (resid -2 through 17 )
76	X-RAY DIFFRACTION	76	chain 'K' and (resid 18 through 42 )
77	X-RAY DIFFRACTION	77	chain 'K' and (resid 43 through 59 )
78	X-RAY DIFFRACTION	78	chain 'K' and (resid 60 through 95 )
79	X-RAY DIFFRACTION	79	chain 'K' and (resid 96 through 162 )
80	X-RAY DIFFRACTION	80	chain 'K' and (resid 163 through 217 )
81	X-RAY DIFFRACTION	81	chain 'L' and (resid 1 through 53 )
82	X-RAY DIFFRACTION	82	chain 'L' and (resid 54 through 67 )
83	X-RAY DIFFRACTION	83	chain 'L' and (resid 68 through 217 )

+
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

-
タンパク質 , 1種, 12分子 ABCDEFGHIJKL

-
非ポリマー , 7種, 825分子

-
詳細

-
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

-タンパク質 , 1種, 12分子 ABCDEFGHIJKL

-非ポリマー , 7種, 825分子

-詳細

-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

-
タンパク質 , 1種, 12分子 ABCDEFGHIJKL

-
非ポリマー , 7種, 825分子

-
詳細

-
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)