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万見

- PDB-6tug: Enterococcus italicus Csm6 bound to cyclic hexa-2'-fluoro-hexa-dAMP -

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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: 6tug

タイトル

Enterococcus italicus Csm6 bound to cyclic hexa-2'-fluoro-hexa-dAMP

要素

CRISPR system endoribonuclease Csm6

キーワード

RNA BINDING PROTEIN / CRISPR / cyclic oligoadenylate / RNase / nuclease

機能・相同性

機能・相同性情報

endonuclease activity / defense response to virus / 加水分解酵素; エステル加水分解酵素
類似検索 - 分子機能

生物種

Enterococcus italicus

手法

X線回折 /

シンクロトロン /

単一同系置換・異常分散 / 解像度: 2.42 Å

データ登録者

Garcia-Doval, C. / Jinek, M.

資金援助

European Union,

スイス,

米国, 3件

組織	認可番号	国
European Research Council (ERC)	ERC-CoG-820152	European Union
Swiss National Science Foundation	205321_169612	スイス
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP1GM128184	米国

引用

ジャーナル: Nat Commun / 年: 2020
タイトル: Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6.
著者: Garcia-Doval, C. / Schwede, F. / Berk, C. / Rostol, J.T. / Niewoehner, O. / Tejero, O. / Hall, J. / Marraffini, L.A. / Jinek, M.

履歴

登録	2020年1月7日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2020年2月26日	Provider: repository / タイプ: Initial release
改定 1.1	2020年4月22日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
改定 1.2	2024年5月15日	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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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	6tug.cif.gz	2.3 MB	表示	PDBx/mmCIF形式
PDB形式	pdb6tug.ent.gz	1.6 MB	表示	PDB形式
PDBx/mmJSON形式	6tug.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/tu/6tug ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tug	HTTPS FTP

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関連構造データ

類似構造データ	6f25-d 6o4w-1 4pqe-1 4xsc-d 4m0f-d 2xuf-d 5hf5-d 6wvo-d 2wu4-d 5g5j-1 Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) Omokage検索で類似形状データを探す (詳細) 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

類似構造データ

Omokage検索で類似形状データを探す (詳細)

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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	#181 - 2015年1月カスケードとCRISPR (Cascade and CRISPR) 類似性 (1)

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集合体

登録構造単位

A: CRISPR system endoribonuclease Csm6

B: CRISPR system endoribonuclease Csm6

C: CRISPR system endoribonuclease Csm6

D: CRISPR system endoribonuclease Csm6

E: CRISPR system endoribonuclease Csm6

F: CRISPR system endoribonuclease Csm6

G: CRISPR system endoribonuclease Csm6

H: CRISPR system endoribonuclease Csm6

ヘテロ分子

417 kDa, 8 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: CRISPR system endoribonuclease Csm6

B: CRISPR system endoribonuclease Csm6

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
104 kDa, 2 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)

C: CRISPR system endoribonuclease Csm6

D: CRISPR system endoribonuclease Csm6

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
104 kDa, 2 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: CRISPR system endoribonuclease Csm6

F: CRISPR system endoribonuclease Csm6

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
104 kDa, 2 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: CRISPR system endoribonuclease Csm6

H: CRISPR system endoribonuclease Csm6

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
104 kDa, 2 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)	93.604, 106.686, 116.793
Angle α, β, γ (deg.)	90.033, 90.007, 90.100
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	CRISPR system endoribonuclease Csm6 / CRISPR type III-A associated protein Csm6 分子量: 50967.016 Da / 分子数: 8 / 由来タイプ: 組換発現由来: (組換発現) Enterococcus italicus (strain DSM 15952 / LMG 22039 / TP 1.5) (バクテリア) 遺伝子: csm6, HMPREF9088_1942 / 細胞株 (発現宿主): BL21 Star / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: E6LHV2, 加水分解酵素; エステル加水分解酵素
#2: 化合物	... ChemComp-AF2 / 2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate) タイプ: DNA linking / 分子量: 349.212 Da / 分子数: 24 / 由来タイプ: 合成 / 式: C₁₀H₁₃FN₅O₆P / タイプ: SUBJECT OF INVESTIGATION
#3: 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: 合成 / 式: SO₄
#4: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 345 / 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	Y

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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: 3.01 Å³/Da / 溶媒含有率: 57.01 %
結晶化	温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法詳細: 100 mM HEPES pH 7.5 1.6 M Ammonium sulphate 25 mM Lithium perchlorate

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器	タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2019年6月15日
放射	プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長	波長: 1 Å / 相対比: 1
反射	解像度: 2.42→48.51 Å / Num. obs: 156394 / % possible obs: 90.8 % / 冗長度: 3.5 % / B_iso Wilson estimate: 37.02 Å² / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.07649 / R_pim(I) all: 0.04726 / R_rim(I) all: 0.0902 / Net I/σ(I): 13.12
反射シェル	解像度: 2.42→2.51 Å / 冗長度: 3.7 % / R_merge(I) obs: 0.4734 / Num. unique obs: 16789 / CC_1/2: 0.781 / CC star: 0.936 / R_pim(I) all: 0.2849 / R_rim(I) all: 0.5536 / % possible all: 97.78

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解析

ソフトウェア

名称	バージョン	分類
PHENIX	1.17.1_3660	精密化
XDS		データ削減
Coot		モデル構築
PHASER		位相決定
autoPROC	1.0.5	データスケーリング

精密化

構造決定の手法:

単一同系置換・異常分散 / 解像度: 2.42→48.51 Å / SU ML: 0.3407 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 30.8114

	R_factor	反射数	%反射
R_free	0.2917	7655	4.9 %
R_work	0.2635	-	-
obs	0.2648	156268	90.85 %

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: 50.78 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.42→48.51 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	27202	0	548	345	28095

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0035	28320
X-RAY DIFFRACTION	f_angle_d	0.7859	38351
X-RAY DIFFRACTION	f_chiral_restr	0.0459	4216
X-RAY DIFFRACTION	f_plane_restr	0.0032	4881
X-RAY DIFFRACTION	f_dihedral_angle_d	21.869	10746

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 (%)
2.42-2.45	0.3316	301	0.3007	5278	X-RAY DIFFRACTION	97.84
2.45-2.48	0.3541	295	0.2975	5333	X-RAY DIFFRACTION	97.76
2.48-2.51	0.3071	235	0.2965	5347	X-RAY DIFFRACTION	97.76
2.51-2.54	0.3718	280	0.3049	5402	X-RAY DIFFRACTION	98
2.54-2.57	0.3163	279	0.2891	5217	X-RAY DIFFRACTION	97.83
2.57-2.61	0.3065	264	0.2983	5391	X-RAY DIFFRACTION	97.99
2.61-2.64	0.3588	248	0.3177	4823	X-RAY DIFFRACTION	95.9
2.69-2.73	0.3611	227	0.3178	4767	X-RAY DIFFRACTION	93.47
2.73-2.77	0.3481	303	0.2952	5295	X-RAY DIFFRACTION	98.06
2.77-2.82	0.3451	257	0.2822	5393	X-RAY DIFFRACTION	98.19
2.82-2.87	0.317	322	0.2781	5288	X-RAY DIFFRACTION	97.92
2.87-2.93	0.3165	304	0.2747	5374	X-RAY DIFFRACTION	98.25
2.93-2.99	0.2936	301	0.2779	5255	X-RAY DIFFRACTION	98.28
2.99-3.05	0.2982	281	0.2757	5370	X-RAY DIFFRACTION	98.59
3.05-3.12	0.3179	310	0.289	5357	X-RAY DIFFRACTION	98.37
3.12-3.2	0.2994	260	0.2749	5326	X-RAY DIFFRACTION	98.57
3.2-3.29	0.2997	265	0.2626	5409	X-RAY DIFFRACTION	98.4
3.29-3.38	0.3046	282	0.2643	5375	X-RAY DIFFRACTION	98.26
3.38-3.49	0.3535	149	0.2613	2823	X-RAY DIFFRACTION	51.9
3.49-3.62	0.2674	268	0.2607	5409	X-RAY DIFFRACTION	98.75
3.62-3.76	0.2855	178	0.2693	3881	X-RAY DIFFRACTION	70.65
3.76-3.93	0.2863	193	0.2688	3798	X-RAY DIFFRACTION	69.31
3.93-4.14	0.2585	270	0.2423	5368	X-RAY DIFFRACTION	98.7
4.14-4.4	0.2176	263	0.2226	5405	X-RAY DIFFRACTION	98.57
4.4-4.74	0.2259	229	0.2123	5386	X-RAY DIFFRACTION	98.61
4.74-5.21	0.2673	291	0.2413	5381	X-RAY DIFFRACTION	98.46
5.21-5.97	0.2726	278	0.2583	5403	X-RAY DIFFRACTION	98.82
5.97-7.51	0.3028	289	0.2855	5366	X-RAY DIFFRACTION	99.05
7.51-10	0.3016	233	0.2549	5393	X-RAY DIFFRACTION	97.96

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	6.2143120573	-1.54726720087	0.841643780856	3.91868014218	0.0561849115141	4.09392194392	-0.0933545927566	0.621342011125	0.493495787648	-0.184588816367	-0.0848168855849	0.0834882990147	-0.4025711797	0.246927533152	0.115853409099	0.297205971462	-0.0483275163643	-0.0404345970437	0.206199738622	0.101781827157	0.287592713138	24.8719426638	-7.98430825831	-6.592725596
2	7.75751318217	-2.10379538307	-1.45405565872	3.25872070982	-1.3390516308	3.01130455762	0.248547051832	0.695440043293	0.734326406068	-0.382200732798	-0.279723900712	-0.53513534489	-0.140713397861	-0.286625139845	-0.00849033185835	0.475464483039	-0.101104528762	0.0195131333162	0.356494176772	0.109397419023	0.461268709955	29.7881667367	-3.98470155652	-10.870444794
3	3.9731045698	-1.7424925393	-2.74411235612	3.68449431366	1.54354407081	8.29554508098	-0.050359680905	-0.0352790361716	-0.325732766496	-0.0364562324035	-0.161954282336	-0.246273754181	-0.200131324297	0.675403562099	-0.0311410955258	0.222840034508	-0.0359034574435	-0.017151643008	0.233559376935	-0.033226480468	0.346448939802	37.3853010601	-14.0601747333	2.90438408597
4	3.05865877161	0.290355084062	1.20606641875	2.67728956631	-0.349777511303	3.767082573	0.049533803368	0.0379496679094	0.324735610602	-0.258760632421	-0.0399301210632	0.149959928246	-0.0587242106566	-0.309740593174	-0.108484529249	0.18606273371	-0.00904396001683	-0.0267443633163	0.238390418284	0.0500222172196	0.337472284865	24.7156405303	-13.9967165151	-0.681622866068
5	5.85224161616	-0.114009623215	-0.300585118605	4.95899747568	-3.89976632273	7.05127354044	-0.000209280561168	0.874564059486	0.405644119213	-0.756519617215	-0.0245880515771	0.354640752288	-0.0257028384362	-0.748621473261	0.158867652282	0.376425679779	0.0662399037926	-0.0982440344145	0.470255339014	-0.0237716990105	0.422703693133	14.8548067794	-9.12340378504	-10.5059148449
6	1.07812863088	0.314845293224	-1.55172707114	2.49384042201	0.0377254071585	7.67847951035	-0.128177358302	0.0382551982121	-0.213536074902	-0.115208315573	0.343630663164	0.0347321013179	-0.100161023811	-0.267153799545	-0.189440462507	0.141162782141	-0.00349762579968	0.0179578452348	0.306407871149	0.0597703709759	0.285671338779	21.6433167951	-25.4525042954	25.4309585576
7	3.07720215951	0.0381400763025	-0.193019588477	1.84774296532	0.511581385134	2.36788559664	0.0125852970907	-0.652760451964	0.128987273645	0.524912593512	-0.166061551628	0.00118290966217	0.0350829679355	-0.141637916066	0.177889909374	0.374122436373	-0.00542689730311	0.0411694494464	0.439560663581	-0.0444123439645	0.321861205959	16.5359242058	-27.915209401	55.1124976591
8	4.22110634276	0.20006030018	-3.20389697894	6.40306813117	-1.04387554346	7.27186217062	-0.238184210804	-0.914352538536	-0.325406447018	1.22232418583	0.31332438389	-0.0989202708834	0.55792996913	-0.837139062211	-0.514345882815	0.80482569834	-0.0458194497496	-0.108673531148	0.911521454119	0.194861320546	0.559073092796	22.8783606707	-38.9627473859	76.5025319894
9	6.16913249624	5.68620545497	-2.95746555954	6.92055510364	-2.74531320079	4.53725538291	0.0944677852926	-0.273402957054	-0.50805789965	1.11480412321	0.00339534049711	-0.410846886983	-0.13679376718	-0.218650555733	-0.0838967656973	0.595393279756	0.0489701402084	-0.0432509750732	0.600470648228	0.0867557118976	0.312107880016	33.0705069378	-36.3288259824	59.2861275033
10	2.35866181816	2.62305965288	1.95857993529	4.64514397917	0.0833872803318	4.49688147293	-0.017737988478	-0.383517855886	-1.74239143968	0.0172174409696	0.0778107256831	-0.575733201099	0.580238558987	0.0855339969339	-0.0313317101994	0.475923956733	0.170133938675	0.112304875017	0.395046534618	0.131890547185	0.443787323926	26.8848717916	-41.0256062268	54.655082867
11	3.46320696423	0.973393256078	-1.02628861053	2.61397804599	-3.35698788107	8.39801873127	-0.154948079079	0.175854562739	-0.392941749126	0.0750398492935	0.307665384867	0.218640209404	0.341215833541	-0.193751058311	0.0734357039715	0.300722522819	0.000547233347464	0.0860208204948	0.415945530074	-0.044777268743	0.375258401385	12.6207307383	-34.5949917923	40.1945429697
12	4.31966292476	-1.37096857526	-0.55450096439	2.91803741277	-0.269782580058	2.63205107512	0.277987003317	0.597117489098	-0.105472932227	-0.563468357506	-0.126471247254	0.249712766789	0.459677052159	-0.0328465879848	-0.139927647655	0.36716292538	-0.045700136834	-0.0238897037456	0.278464281213	-0.0881744481883	0.301122290911	26.7928169177	-41.6526564203	-9.63286994407
13	1.66231213484	0.291151395355	0.442789240809	5.49700646093	-1.37950575828	3.16681577917	-0.00950472936727	-0.0302174735418	-0.34957766973	-0.010274941033	0.158153844669	0.560842025683	0.0951877204	-0.219457769383	-0.154289385742	0.225262754037	-0.0731748862526	-0.0213288703451	0.319997587669	-0.00774697265039	0.393732301724	19.7580176867	-39.2019965501	1.88888432662
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50	0.846619161902	0.0388536844219	0.602410642355	0.829599769645	-0.444511393497	2.48588560627	0.00351760284722	-0.0423640995961	-0.135758946495	0.185231150557	0.033510526463	0.0310874747562	0.0531590152732	-0.0521853184441	-0.0639925623782	0.180159229367	0.0384401849352	0.030161137369	0.23689225631	-0.0163580714022	0.287644944778	28.2961106582	18.1098412458	135.460458664
51	2.19845944172	-0.478683111115	-0.197056889539	0.893193339377	-0.321036234656	4.1883381153	-0.00882469096471	0.818052283662	0.23081541521	-0.300574747915	-0.0384135813211	-0.0766526962116	-0.08319671671	-0.183543234559	0.0419005203974	0.369292700374	-0.0361971446996	-0.0183090084025	0.489386921906	0.069007552345	0.408689222905	21.8406865885	38.646222826	80.90824745
52	1.14812433253	0.130340266717	-0.0540694476515	1.52173585237	-0.61182781251	1.77369589604	0.00751877704628	-0.192412177974	-0.218031346601	0.290965524831	-0.0253768168451	-0.0249399381346	0.210119765083	0.0752672127448	0.0296580604237	0.302352391805	0.0201310105928	0.00615509263101	0.288203852614	0.0123960456088	0.343459821662	75.4106486457	16.6086115386	82.4091119406
53	2.13084217625	-0.298451718705	-0.271414884007	1.23378497133	0.0595804353849	2.06272458833	0.0109304731277	0.775119816516	0.137014897407	-0.46001546516	-0.0848040002716	-0.124592248641	-0.283242260909	-0.0170754506422	0.0669362140017	0.406742773118	-0.0131644519951	-0.00484007505401	0.549278998389	0.0650340741097	0.357810790702	70.3295382001	37.0495886806	25.7603095169
54	3.48499137215	0.983025256635	-0.318831720168	3.0863611542	-0.931681327613	4.01764144217	0.193151732658	-0.254074131529	0.0498153793764	0.519967320406	-0.186454008945	0.0187820439565	-0.483881627846	0.142389753053	-0.0201093587238	0.312459211534	0.0464401844341	0.0206202814427	0.188674319967	-0.0833750863808	0.287717571364	78.5282271197	45.0230419576	89.7979557526
55	4.90171731274	4.01463044462	3.0421395409	7.86127256297	2.60789554516	2.94615482742	-0.0903771331544	-0.434904253937	0.212868877624	0.739455228275	0.101070360771	0.0115168482696	-0.326772256027	-0.162673982614	-0.0399954323785	0.433208719424	0.0907132076565	0.0327156513299	0.332626436023	-0.0474068251261	0.332768571261	71.7996975636	46.9483194639	91.267104142
56	2.42007393318	1.75358746118	-0.515263763037	4.25549629989	-1.76909160549	3.78591589921	0.00599605173748	0.022105501441	0.0528956726254	0.159864663239	0.222345328918	0.28066353948	0.00237979512879	0.0525955298249	-0.277898798736	0.225915340937	0.0232149902999	-0.0174246224436	0.146119127141	-0.0137952951473	0.315564799861	74.259381011	39.7504054653	77.3518559293
57	3.38222663971	0.656397818351	2.09577196082	3.89716708651	1.59627616436	6.53559968152	-0.0609090039421	-0.664779837464	-0.0391265854369	0.537570659835	-0.115684002305	-0.44647295933	-0.470162265957	0.371204974767	0.171332346291	0.379821258153	-0.0856779974279	-0.0428189535107	0.430350530368	0.028460404723	0.437135082749	85.2447182016	42.4335379015	92.4245346357
58	2.97932132391	-0.865713410024	-2.50185375926	2.5814644387	0.997365458958	6.18493706614	-0.0297124626399	-0.336906201545	-0.0498461144315	0.165693746539	0.248136092158	-0.184918245928	0.104266026883	0.127139511503	-0.215897828266	0.16851934203	0.020647283783	0.000535181027717	0.227016339795	0.0147498531371	0.213934347609	85.4782704027	28.1036737389	58.1417917896
59	4.67214829499	-0.221293561257	-2.53026877754	1.58397197865	-0.431674275631	9.14537078799	-0.132883233529	0.1311771562	1.03120906902	-0.0426888059538	0.26754637342	0.0787738654479	0.248771141391	0.523650151636	-0.106043676106	0.218708302875	-0.0530541157785	-0.0336963023054	0.367596583965	0.0444752172706	0.508274945574	96.3529378871	29.8467092282	41.4669626327
60	9.15240998095	-0.0214949879067	-7.84819026893	2.55036277169	0.0481388001058	9.18963067836	-0.21458814725	0.568520215021	0.25832438079	0.317702334982	0.410407693246	0.00283619405262	0.709298026324	0.22462812299	-0.00713528391722	0.30823160805	0.00675471311053	-0.0464600622124	0.400126501664	-0.085429280965	0.328187486367	88.8522738182	22.3745171446	34.0757799305
61	3.19968958795	-0.605035311215	-1.26055129385	6.70474217357	1.15390804731	7.29899552023	0.419576702944	0.55073536164	0.289646889116	-0.975649485983	0.112421698509	-0.200602953078	-0.808700439537	0.0793382608768	-0.399937647952	0.338138230592	-0.029108216516	-0.0233913531403	0.447088969253	-0.00882167109089	0.214385429124	88.5731098486	21.0996987241	22.9782458492
62	5.82344416699	-2.03411769496	-0.491036416638	4.27536110921	-1.1494923864	3.83896798421	-0.0277320441533	0.870732645013	0.401527729369	-0.722132912939	-0.300336291502	-0.272739246649	-0.0560225363111	-0.210723993614	0.522464924101	0.551384771535	-0.0221389962739	-0.017544163072	0.87231485392	0.0791692716056	0.41598349164	93.3374818625	21.7713896286	5.20623624668
63	3.42212457097	1.19427258764	-0.102468520133	2.10898628594	2.31728620189	3.91453829539	-0.0627587705889	0.968650281172	0.216993479871	-1.08681684504	0.841991353484	-0.575007083606	-0.538869135907	0.943418364427	-0.646091022892	0.548087643579	-0.0366804465546	0.190137261546	1.17082046195	-0.16285093929	0.561458561281	86.9764701322	20.1626321331	7.00359168109
64	7.32717879653	-2.22186587161	-1.01504163666	4.74932164999	-1.08883991957	4.40370879767	0.0467293712548	0.900085009283	-1.13797902637	-0.242760190404	-0.279492570358	0.290382919994	0.140082623198	-0.259219768041	0.28584679809	0.346366536992	-0.0156925087278	0.00770939860373	0.460740644756	-0.159922627162	0.364021990607	79.865741839	14.17641987	24.5656343876
65	3.75306646941	-1.27853570867	-4.94342600195	2.98763861499	3.15242405964	8.37857295932	-0.197761164948	0.0722966576272	-0.693302430155	0.134639552241	-0.304309815124	0.00279944487811	0.374167958889	0.00755411935003	0.350489278473	0.250116994545	0.0122048474875	-0.00857000283123	0.319705869837	0.0137807628969	0.425324622367	95.5187456754	18.6636815613	43.8649112309

精密化 TLSグループ

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 155 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 156 through 180 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 181 through 215 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 216 through 309 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 310 through 356 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 357 through 385 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 386 through 407 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 408 through 430 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 100 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 101 through 127 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 128 through 180 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 181 through 246 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 247 through 267 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 268 through 290 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 291 through 319 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 320 through 356 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 357 through 385 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 386 through 407 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 408 through 430 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid -1 through 20 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 21 through 246 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 247 through 267 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 268 through 309 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 310 through 356 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 357 through 407 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 408 through 430 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 0 through 44 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 45 through 82 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 83 through 215 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 216 through 246 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 247 through 267 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 268 through 309 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 310 through 356 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 357 through 407 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 408 through 430 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid -1 through 20 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 21 through 64 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 65 through 100 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 101 through 127 )
44	X-RAY DIFFRACTION	44	chain 'E' and (resid 128 through 179 )
45	X-RAY DIFFRACTION	45	chain 'E' and (resid 180 through 215 )
46	X-RAY DIFFRACTION	46	chain 'E' and (resid 216 through 267 )
47	X-RAY DIFFRACTION	47	chain 'E' and (resid 268 through 356 )
48	X-RAY DIFFRACTION	48	chain 'E' and (resid 357 through 385 )
49	X-RAY DIFFRACTION	49	chain 'E' and (resid 386 through 430 )
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 0 through 246 )
51	X-RAY DIFFRACTION	51	chain 'F' and (resid 247 through 430 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid -1 through 215 )
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 216 through 430 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 0 through 44 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 45 through 82 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 83 through 127 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 128 through 179 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 180 through 215 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 216 through 246 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 247 through 267 )
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 268 through 290 )
62	X-RAY DIFFRACTION	62	chain 'H' and (resid 291 through 321 )
63	X-RAY DIFFRACTION	63	chain 'H' and (resid 322 through 352 )
64	X-RAY DIFFRACTION	64	chain 'H' and (resid 353 through 407 )
65	X-RAY DIFFRACTION	65	chain 'H' and (resid 408 through 430 )

+
万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

すべてのお知らせ

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)

-ムービー

-構造ビューア

+ビューアのログ

-このページ

-このウェブサイト

-オプション

+データを開く

-基本情報

-構造の表示

-ダウンロードとリンク

-ダウンロード

-検証レポート

-関連構造データ

-リンク

-集合体

-要素

-実験情報

-実験

-試料調製

-データ収集

-解析

+万見について

-お知らせ

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

-2020年8月12日: 新型コロナ情報

+2020年3月5日: 新型コロナウイルスの構造データ

+2019年1月31日: EMDBのIDの桁数の変更

+2017年7月12日: PDB大規模アップデート

-万見 (Yorodumi)

-
ムービー

-
構造ビューア

+
ビューアのログ

-
このページ

-
このウェブサイト

-
オプション

+
データを開く

-
基本情報

-
構造の表示

-
ダウンロードとリンク

-
ダウンロード

-
検証レポート

-
関連構造データ

-
リンク

-
集合体

-
要素

-
実験情報

-
実験

-
試料調製

-
データ収集

-
解析

+
万見について

-
お知らせ

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

-
2020年8月12日: 新型コロナ情報

+
2020年3月5日: 新型コロナウイルスの構造データ

+
2019年1月31日: EMDBのIDの桁数の変更

+
2017年7月12日: PDB大規模アップデート

-
万見 (Yorodumi)