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- PDB-8cso: Crystal Structure of Orotidine 5'-phosphate decarboxylase from Kl... -

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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: 8cso

タイトル

Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Uridine-5'-monophosphate

要素

Orotidine 5'-phosphate decarboxylase

キーワード

LYASE / SSGCID / Klebsiella pneumoniae / Orotidine 5'-phosphate decarboxylase / decarboxylation / uridine-5'-monophosphate / pyrF / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

機能・相同性

機能・相同性情報

orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
類似検索 - 分子機能

生物種

Klebsiella pneumoniae subsp. pneumoniae HS11286 (肺炎桿菌)

手法

X線回折 /

シンクロトロン /

分子置換 / 解像度: 2.6 Å

データ登録者

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

資金援助

米国, 1件

引用

ジャーナル: to be published
タイトル: Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Guanosine-5'-monophosphate
著者: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

履歴

登録	2022年5月13日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2022年6月8日	Provider: repository / タイプ: Initial release
改定 1.1	2023年10月18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	8cso.cif.gz	972.9 KB	表示	PDBx/mmCIF形式
PDB形式	pdb8cso.ent.gz	671.8 KB	表示	PDB形式
PDBx/mmJSON形式	8cso.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/cs/8cso ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8cso	HTTPS FTP

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関連構造データ

関連構造データ	1eixS S: 精密化の開始モデル
類似構造データ	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	#254 - 2021年2月セルロース合成酵素 (Cellulose Synthase) 類似性 (1) #86 - 2007年2月エキソソーム (Exosomes) 類似性 (1) #228 - 2018年12月酵素の指向性進化 (Directed Evolution of Enzymes) 類似性 (1)

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集合体

登録構造単位

A: Orotidine 5'-phosphate decarboxylase

B: Orotidine 5'-phosphate decarboxylase

C: Orotidine 5'-phosphate decarboxylase

D: Orotidine 5'-phosphate decarboxylase

E: Orotidine 5'-phosphate decarboxylase

F: Orotidine 5'-phosphate decarboxylase

G: Orotidine 5'-phosphate decarboxylase

H: Orotidine 5'-phosphate decarboxylase

I: Orotidine 5'-phosphate decarboxylase

J: Orotidine 5'-phosphate decarboxylase

ヘテロ分子

259 kDa, 10 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: Orotidine 5'-phosphate decarboxylase

B: Orotidine 5'-phosphate decarboxylase

ヘテロ分子

登録者が定義した集合体
根拠: gel filtration
52.1 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: Orotidine 5'-phosphate decarboxylase

D: Orotidine 5'-phosphate decarboxylase

ヘテロ分子

登録者が定義した集合体
51.8 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: Orotidine 5'-phosphate decarboxylase

F: Orotidine 5'-phosphate decarboxylase

ヘテロ分子

登録者が定義した集合体
52.1 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: Orotidine 5'-phosphate decarboxylase

H: Orotidine 5'-phosphate decarboxylase

登録者が定義した集合体
51.4 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)

I: Orotidine 5'-phosphate decarboxylase

J: Orotidine 5'-phosphate decarboxylase

登録者が定義した集合体
51.4 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)	61.710, 91.310, 127.730
Angle α, β, γ (deg.)	100.942, 100.364, 91.113
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
d_1	ens_1	(chain "A" and ((resid -1 and (name N or name...
d_2	ens_1	(chain "B" and ((resid -1 and (name N or name...
d_3	ens_1	(chain "C" and ((resid -1 and (name N or name...
d_4	ens_1	(chain "D" and ((resid -1 and (name N or name...
d_5	ens_1	(chain "E" and ((resid -1 and (name N or name...
d_6	ens_1	(chain "F" and ((resid -1 and (name N or name...
d_7	ens_1	(chain "G" and (resid -1 through 26 or (resid 27...
d_8	ens_1	(chain "H" and ((resid -1 and (name N or name...
d_9	ens_1	(chain "I" and (resid -1 through 15 or (resid 16...

NCSドメイン領域:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	HIS	ILE	A	2 - 177
d_1	2	ens_1	MET	ILE	A	191 - 206
d_1	3	ens_1	PRO	ARG	A	216 - 228
d_2	1	ens_1	HIS	ILE	C	2 - 177
d_2	2	ens_1	MET	ILE	C	191 - 206
d_2	3	ens_1	PRO	ARG	C	216 - 228
d_3	1	ens_1	HIS	ILE	F	2 - 177
d_3	2	ens_1	MET	ILE	F	191 - 206
d_3	3	ens_1	PRO	ARG	F	216 - 228
d_4	1	ens_1	HIS	ILE	I	3 - 178
d_4	2	ens_1	MET	ILE	I	184 - 199
d_4	3	ens_1	PRO	ARG	I	209 - 221
d_5	1	ens_1	HIS	ILE	J	3 - 178
d_5	2	ens_1	MET	ILE	J	192 - 207
d_5	3	ens_1	PRO	ARG	J	217 - 229
d_6	1	ens_1	HIS	ILE	M	3 - 178
d_6	2	ens_1	MET	ILE	M	192 - 207
d_6	3	ens_1	PRO	ARG	M	217 - 229
d_7	1	ens_1	HIS	ARG	O	2 - 206
d_8	1	ens_1	HIS	ILE	P	2 - 193
d_8	2	ens_1	PRO	ARG	P	200 - 212
d_9	1	ens_1	HIS	ILE	Q	1 - 176
d_9	2	ens_1	MET	ILE	Q	179 - 194
d_9	3	ens_1	PRO	ARG	Q	204 - 216

NCS oper:

ID	Code	Matrix	ベクター
1	given	(-0.972356359361, 0.143940022022, -0.183859676031), (0.130030794573, -0.32022446506, -0.938375343048), (-0.193946133947, -0.936342652044, 0.29265565959)	72.346593814, -75.570320773, -44.3225930397
2	given	(-0.719249356674, 0.645886743533, -0.25595053712), (-0.0615028680001, 0.307766062534, 0.949472194422), (0.692024392744, 0.698648957116, -0.181636655353)	24.6129288668, 38.7318778534, -12.7525970114
3	given	(0.852759281364, 0.0184514614577, -0.521978114118), (0.0254880536886, -0.999655255677, 0.00630308788187), (-0.521681863943, -0.0186792228894, -0.852935589283)	-62.5299648967, -35.2752499657, -10.6047465165
4	given	(0.34085033316, 0.632748991724, -0.695305518356), (-0.510821329776, 0.745541856845, 0.428052460264), (0.789229129867, 0.209275065796, 0.577339871657)	-11.6942298142, 26.611022804, 38.2374521827
5	given	(-0.166973393126, 0.463591384564, -0.870174071175), (0.525261715091, -0.705069769595, -0.476420770604), (-0.83439799655, -0.536618717677, -0.125778913938)	-3.12894998511, -86.6421653052, 54.4974042792
6	given	(0.610831223561, -0.647560050481, 0.455577871877), (-0.659663557416, -0.734445860296, -0.159478115463), (0.437868938542, -0.203113907243, -0.875794230025)	-26.4111740392, -2.32345203694, 21.1772168918
7	given	(-0.736567123074, -0.160874483146, 0.65695378367), (0.589568276254, 0.323312425501, 0.740188032294), (-0.331478688367, 0.932517279298, -0.143294811383)	46.4603955191, 11.5181361287, 109.081699976
8	given	(-0.535003488818, -0.602169227565, 0.592590489567), (-0.545783740386, -0.28906788168, -0.786485771334), (0.644896406938, -0.744198885483, -0.174001848162)	11.5208582582, -72.2974673347, -35.8499435928

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要素

#1: タンパク質	Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase 分子量: 25686.488 Da / 分子数: 10 / 断片: KlpnC.01229.a.B1 / 由来タイプ: 組換発現由来: (組換発現) Klebsiella pneumoniae subsp. pneumoniae HS11286 (肺炎桿菌) 株: HS11286 / 遺伝子: pyrF, KPHS_21850 / プラスミド: KlpnC.01229.a.B1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) 参照: UniProt: A0A0H3GNE4, orotidine-5'-phosphate decarboxylase
#2: 化合物	ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / UMP 分子量: 324.181 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C₉H₁₃N₂O₉P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル分子量: 62.068 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C₂H₆O₂
#4: 水	ChemComp-HOH / water 分子量: 18.015 Da / 分子数: 227 / 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: 2.71 Å³/Da / 溶媒含有率: 54.6 %
結晶化	温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: RigakuReagents JCSG Top96 screen, conditon D12: 1000mM sodium citrate tribasic, 100mM CHES/NaOH pH 9.5; KlpnC.01229.a.B1.PW39025 at 18mg/ml + 3m UMP; tray 322516 d12: cryo: 20% EG + 3mM UMP: puck dnf8-2.

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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: 0.97872 Å

検出器

タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2022年2月24日 / 詳細: Beryllium Lenses

放射

モノクロメーター: Diamond [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: 0.97872 Å / 相対比: 1

反射

解像度: 2.6→50 Å / Num. obs: 81130 / % possible obs: 98 % / 冗長度: 3.935 % / B_iso Wilson estimate: 53.319 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.084 / Χ²: 0.919 / Net I/σ(I): 14.65

反射シェル

Diffraction-ID: 1

解像度 (Å)	冗長度 (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.6-2.67	3.981	0.632	2.11	5990	0.768	0.731	97.5
2.67-2.74	3.977	0.51	2.66	5766	0.847	0.589	97.4
2.74-2.82	3.98	0.414	3.25	5688	0.886	0.478	97.6
2.82-2.91	3.976	0.341	3.95	5508	0.914	0.394	97.9
2.91-3	3.971	0.256	5.15	5341	0.952	0.296	97.9
3-3.11	3.969	0.211	6.25	5242	0.967	0.244	98
3.11-3.22	3.959	0.161	8.19	4992	0.978	0.186	98.1
3.22-3.36	3.951	0.115	11.42	4794	0.988	0.133	98.1
3.36-3.51	3.944	0.094	13.62	4608	0.992	0.109	98.3
3.51-3.68	3.933	0.07	17.54	4412	0.995	0.081	98.3
3.68-3.88	3.927	0.058	20.64	4225	0.996	0.067	98.4
3.88-4.11	3.915	0.048	23.99	4001	0.997	0.055	98.4
4.11-4.39	3.908	0.043	26.58	3744	0.998	0.05	98.6
4.39-4.75	3.899	0.036	30.1	3490	0.998	0.042	98.4
4.75-5.2	3.891	0.035	30.59	3191	0.998	0.041	98.7
5.2-5.81	3.876	0.041	27.77	2896	0.998	0.047	98.8
5.81-6.71	3.868	0.038	29.99	2550	0.998	0.044	98.5
6.71-8.22	3.837	0.03	35.46	2160	0.999	0.034	98.8
8.22-11.63	3.811	0.022	42.46	1664	0.999	0.026	97.8
11.63-50	3.49	0.026	39.96	868	0.999	0.03	93.2

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解析

ソフトウェア

名称	バージョン	分類
XDS		データ削減
XSCALE		データスケーリング
PHENIX	1.20.1	精密化
PDB_EXTRACT	3.27	データ抽出
MoRDa		位相決定
Coot		モデル構築

精密化

構造決定の手法:

分子置換
開始モデル: pdb entry 1eix as per MoRDa

1eix

解像度: 2.6→48.34 Å / SU ML: 0.3525 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 25.0824
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2

	R_factor	反射数	%反射	Selection details
R_free	0.2348	1958	2.41 %	0
R_work	0.1974	79151	-	-
obs	0.1983	81109	98.08 %	-

溶媒の処理

減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL

原子変位パラメータ

B_iso mean: 68.99 Å²

精密化ステップ

サイクル: LAST / 解像度: 2.6→48.34 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	15689	0	117	227	16033

拘束条件

Refine-ID	タイプ	Dev ideal	数
X-RAY DIFFRACTION	f_bond_d	0.0045	16080
X-RAY DIFFRACTION	f_angle_d	0.6984	21914
X-RAY DIFFRACTION	f_chiral_restr	0.049	2617
X-RAY DIFFRACTION	f_plane_restr	0.0062	2910
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5887	5594

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	タイプ	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.4173378982
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.473746358348
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.10859272941
ens_1	d_5	A	X-RAY DIFFRACTION	Torsion NCS	0.90327622412
ens_1	d_6	A	X-RAY DIFFRACTION	Torsion NCS	0.956748410186
ens_1	d_7	A	X-RAY DIFFRACTION	Torsion NCS	0.988526437308
ens_1	d_8	A	X-RAY DIFFRACTION	Torsion NCS	0.986096962042
ens_1	d_9	A	X-RAY DIFFRACTION	Torsion NCS	0.996929646288

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 (%)
2.6-2.67	0.3347	145	0.2956	5618	X-RAY DIFFRACTION	97.43
2.67-2.74	0.269	127	0.2666	5614	X-RAY DIFFRACTION	97.55
2.74-2.82	0.2794	147	0.2432	5625	X-RAY DIFFRACTION	97.65
2.82-2.91	0.2974	151	0.2397	5635	X-RAY DIFFRACTION	97.72
2.91-3.01	0.3025	135	0.2379	5625	X-RAY DIFFRACTION	97.93
3.01-3.13	0.2869	138	0.251	5664	X-RAY DIFFRACTION	98.01
3.13-3.28	0.2546	118	0.2195	5719	X-RAY DIFFRACTION	98.23
3.28-3.45	0.2379	128	0.2033	5659	X-RAY DIFFRACTION	98.18
3.45-3.66	0.2423	121	0.1935	5686	X-RAY DIFFRACTION	98.46
3.66-3.95	0.2291	164	0.1834	5632	X-RAY DIFFRACTION	98.39
3.95-4.34	0.2009	131	0.1689	5714	X-RAY DIFFRACTION	98.57
4.34-4.97	0.1922	168	0.164	5639	X-RAY DIFFRACTION	98.57
4.97-6.26	0.2386	139	0.1955	5699	X-RAY DIFFRACTION	98.82
6.26-48.34	0.2048	146	0.1699	5622	X-RAY DIFFRACTION	97.61

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	6.07519366402	1.43805766182	0.975559747951	4.71860252005	-1.80704712555	5.27346794812	-0.11211240597	0.738743856115	0.285571211902	-0.621979101239	0.466648670656	0.309028721611	-0.522743509425	-0.985662514717	-0.280350993487	0.513825218773	0.0257278955808	-0.0797135287856	0.583130845424	0.138136042894	0.42707148555	22.714336762	-15.8764418441	-44.121361398
2	2.92198922729	-0.127592946634	-0.0133424140961	2.29669316612	-0.00434221945921	4.48599094674	-0.0285094742495	0.033584059154	-0.0194260225965	0.0413285269218	0.0259869488711	0.270907204877	0.0901703945072	-0.498699306542	0.0105937032096	0.310776133336	-0.0167506359043	-0.0228161676526	0.324783587377	0.0237478664605	0.307381514773	28.3325647071	-22.0635947109	-30.7249694729
3	5.18071215183	-0.564993790268	-2.00248452612	6.24033990538	0.204456137725	6.17381274715	0.19140628462	0.327328373979	0.0252355351112	-0.0975729632052	-0.263880997225	-1.12824744503	-0.150941492945	1.02839491191	0.0691128056838	0.402190059488	-0.028077505512	-0.0513348500874	0.744280317891	0.0418083125568	0.510951692759	57.1243655227	-25.889528166	-47.4484348208
4	2.56034497606	0.505254841905	-0.626224159204	2.32902986879	0.515858067739	3.31573704778	-0.0333507910527	0.361691259797	0.0352126791041	-0.0825293131802	0.104251193057	0.111588922397	0.269214830843	0.214393610487	-0.0675250208594	0.450547176824	0.00988039008443	-0.00546906943677	0.438993158319	0.0174249798538	0.290681650783	42.288025621	-29.145278042	-45.5713901868
5	3.47501520717	-0.863830521413	-0.0386068263946	3.55604262015	0.273396657179	4.11316859195	-0.121805957074	-0.250848118482	-0.493321387523	0.234497400444	0.155661992495	0.0400769523783	0.715245008668	0.27692983549	-0.0214776466772	0.594166193327	0.0238933413671	0.00318050202435	0.342313459942	0.0476203214244	0.37862004646	42.4726893592	-41.9992161644	-34.0498396348
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7	7.43986861757	1.22014714434	0.390254053833	3.83035305796	-3.41711476479	8.23009421716	-0.348112354118	-0.0575127442551	-0.066597831002	-0.246358839631	-0.0845952914606	-0.946556469141	0.88272939906	1.44875170452	0.60703799527	0.621438649553	0.180402593035	0.062670123195	1.41934347966	-0.156651140719	0.694777211144	66.8251798432	-33.9844011902	-43.8632494512
8	2.30252854179	-0.907368782271	-0.649840689464	4.51453380448	-1.11349228167	2.37703123511	-0.129359311952	-0.205077424163	-0.179748126037	0.00600559182078	0.20181673318	-0.789490774682	0.20460074039	0.347384352597	-0.0822604655745	0.242039485011	0.0104638425515	-0.0246575322255	0.39134065751	0.0132830336269	0.434433698029	10.6769096295	-10.0134203365	-0.419794694358
9	2.79708791516	0.169927450716	-0.0268991023226	1.34952311002	0.0483918003958	2.3153556944	0.0996436488353	-0.351483595342	0.0944395043171	0.147458456511	-0.0709428136078	-0.0850975248523	-0.0195961576683	0.13515819815	-0.0380750572213	0.266260216808	0.00609324352483	0.00907643363686	0.332311686337	0.0183983667752	0.366770046094	-2.5934737869	-5.39523500291	6.10583358386
10	8.77006759007	0.523837996495	4.48725257121	4.44029560607	-0.0594984031934	8.72426932457	-0.0224873010066	-1.19874250842	0.850818325185	0.35716256303	-0.0242451301258	0.13150563584	-0.545620793581	-0.388188852615	0.112425224298	0.345830688731	0.0442524118636	0.0745442009335	0.389864721231	-0.0711699926124	0.386486935129	-10.0220841493	6.63109306078	11.1924603905
11	1.97835588576	-0.627686221875	0.843944993939	2.78105209222	-1.38254713419	2.79940551595	-0.0165586081934	0.394574142412	0.286180251619	-0.61185286374	-0.0807354211774	0.321532984666	0.261159427304	0.103395013506	0.159639705877	0.328911055949	-0.0159607643282	-0.0136429805171	0.287273128097	0.0485442164636	0.388496933128	-11.1895920641	1.94792230526	-10.5116894434
12	3.23929152749	-0.108439829502	-1.24340697289	4.75442288984	2.26759437147	1.99839942215	0.0758529823771	0.444936342386	0.247464882638	-0.487821097368	0.163199285103	0.693837364023	-0.774166421698	-0.616587539476	-0.395446987056	0.44323135034	0.0298540199663	-0.0248122504173	0.29678914185	0.131970647982	0.558038671678	-11.5032486667	10.5547518651	-7.17448399397
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21	6.28362440034	0.19163499705	0.621318867197	0.777542221162	-1.31641856395	5.55575521138	-0.291589276474	-0.705334786203	0.704037872907	0.231290864867	0.189002775046	-0.035736308283	-0.271451529781	-0.527174977892	0.0812846029154	0.179854092701	0.00107519823734	-0.0080164009488	0.415560373189	-0.0337570092304	0.381805756394	-21.9101511998	-8.94125695452	-1.82567918015
22	5.00648770286	6.24345789636	2.38638754916	7.84609203166	2.77366730094	1.64230140482	-1.36320437017	0.263919695478	3.1489261079	0.211062745027	0.303043539691	1.82508857116	-1.55858184486	0.797922146867	0.992888462466	0.817633098201	-0.00347794592871	-0.0438067169256	0.593761584909	0.104971473196	1.13578856846	-24.8712964004	7.04269008149	-6.08231558461
23	4.31090038763	-0.174049245578	-1.51536479481	1.2440590201	0.364873723223	4.40765171174	0.0395740944055	0.185690539587	0.572874194796	-0.0280444477038	0.08010817207	0.197464505119	-0.218994655429	-0.354720428413	-0.0969240052539	0.241624711911	0.0145307409484	-0.00270825171692	0.285724423839	0.0528340484619	0.328680935151	-28.9520344227	-9.64592389298	-8.62344589409
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25	3.76142980933	1.45370394608	-0.211637662525	1.65559642714	0.842753200726	3.64538585861	0.0456181496193	0.130776296915	0.047494866693	0.205129164181	0.111539578379	0.595698277348	0.192930836046	-0.607691301569	0.016177955367	0.265791658318	0.0308128959257	0.0213071300516	0.383830097529	0.097972058055	0.385829269391	-34.2356775595	-16.6759925954	5.18839989612
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30	4.83163287433	-0.0256429365986	0.623046409854	3.4981147579	-0.899957791691	4.25214057773	0.367704213429	-0.129634779841	-0.452353834939	0.111453592356	-0.325837161439	-0.75365909894	0.428088413377	0.823455863124	-0.031809125716	0.4586721789	0.0969648554636	-0.00106305574318	0.685820120137	0.0305879767755	0.364808323999	24.9544889285	-42.9357715056	50.153274975
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41	0.887777268939	1.76126823877	-0.715417926384	3.79848018011	-0.807302160408	1.77132831822	0.345980478331	0.621106375751	1.16643534747	-0.481962592586	0.323803034668	0.169163929178	-0.236506706945	-1.77531388066	-0.607940451989	0.815258491718	0.423871308383	0.304118791951	1.65760651147	-0.063998870666	1.24074966962	-23.2738983196	4.20055895036	60.2092487884
42	0.0604441584486	0.0912598496469	-0.148427020054	2.00484106811	0.0186122689445	0.620395125138	0.263843718369	-0.335161566456	-0.798068689517	0.164633036896	0.0598193060517	0.132917095298	0.804516425431	-0.291416251302	0.0379203934421	1.76765585973	-0.473452887488	-0.241220266102	0.724530156537	0.430391318974	1.47710567699	3.29791284164	-14.0061760531	93.1945316869
43	4.53663596369	0.848342430741	0.403094095713	2.6598255876	0.392884852286	2.91177565765	0.334963805539	-0.63197651784	-0.344852810418	0.690487390463	-0.348501732393	0.346376122553	-0.502434806094	-0.564695138847	-0.0420876162113	1.16185681688	-0.17162422472	0.168278014937	0.650518745907	-0.0931153262808	0.5968255611	-1.80763051503	-1.55243928225	85.6978581765
44	3.51442781901	1.62384981544	0.865754510255	2.02797017122	1.51649394879	4.50089209566	0.373245658622	-0.135851395839	0.265540650703	0.360489190387	-0.163649791158	-0.109463926043	-0.921041859349	-0.134727422836	0.00499940530968	1.24063027932	-0.0692520651863	0.134781800816	0.440970432711	-0.121017649478	0.568177014151	4.12014727603	7.53468231203	81.8971266992
45	6.93411779138	-5.66538339578	-5.65961042168	6.91792942824	3.55487099708	7.03970121302	0.186102386544	2.58079987996	-0.831658859643	-1.32338610586	0.759694258307	-0.403076232483	-0.222313066792	0.40701736104	-0.739006848094	1.28467325812	0.0142542680261	0.147379540775	1.76705609953	-0.589528592802	1.04710465532	15.0786311171	-1.54273565272	63.1656759378
46	8.0067763773	2.43798405655	0.227741912646	0.991427586061	-1.22620627846	6.75548809964	0.174764365869	0.400288006521	-0.70955336425	1.52060843151	-0.059672340505	-0.662814491443	1.09395487359	0.70292620746	-0.188665461696	1.29038608826	-0.069633378785	0.00236083540898	0.51464092736	-0.154722784745	0.666423940678	14.044559338	6.67867011692	77.702628687
47	2.42936803706	0.688456587947	1.71956020336	1.85672032491	0.473857766005	3.8597839492	0.1554768857	0.211024006495	-0.812280943526	0.197919609879	-0.103542492526	-1.66758776126	1.56880110753	-0.669676339995	-0.11846232238	1.04488752444	-0.117527713764	0.0184843820599	0.551012989063	-0.240992566099	0.965692689923	20.2043240066	4.54866768464	84.4175029352
48	0.348848376347	-0.185462318742	0.227466198299	1.56925085244	-3.00653766302	5.80582323113	-0.241203865605	-0.670683599646	-0.488806865289	-0.0611740436534	-0.416844869892	0.0981072869236	-0.325478762785	0.422002963007	0.538776528256	1.25662819014	-0.108779315289	0.0296088380737	0.537340665609	0.0688848502358	1.25922944973	16.636138698	-10.2175027329	92.2838931184
49	1.63524311646	1.29869020258	-1.15444425658	4.0188752001	-1.88051183901	1.10534176898	0.23123656217	0.694866256914	1.33373449079	-0.467323332247	0.298931481295	-0.0166803322209	0.0764040806	-0.576861296898	-0.57798181068	1.3597071884	0.371809864983	-0.289518532649	0.856989083736	-0.0360670389939	1.37514752019	-17.5831734836	-43.3496043166	-1.97600863038
50	3.5573439864	1.14936976652	-1.17622989162	3.12597634343	-0.123251620367	1.5332963068	-0.18828542552	-0.0931872229783	1.09688320051	-0.653611411355	-0.0369394329818	1.2115001288	-0.119672297478	-0.758495989416	-0.0803684388653	0.958804992366	0.165340598334	-0.280891222486	1.05624916884	-0.165496012943	1.39077227289	-22.0980195836	-49.9694177496	5.39332164827
51	1.79142562157	1.50660742287	0.279786864278	2.89480745946	-0.894913269276	2.07298314828	-0.0195911779789	0.264165439139	-0.00654184923409	-0.317799134771	-0.0210255492834	0.658419641519	0.211691518423	-0.839599325599	-0.0171023860521	0.823808155016	0.141058668312	-0.278845830765	1.09176653318	-0.602044650739	1.3087879945	-17.2392651037	-60.4737342892	8.77373338918
52	2.86072832562	-0.196212152267	1.25882838729	1.87868142854	-0.711368358528	5.66612903548	-0.249734005747	-0.00118998209059	-0.0499342343889	-0.250075882657	-0.456872082316	0.771165518877	0.398361911362	-1.09680596303	0.325756798933	0.78449785019	-0.0450889233381	-0.18456810927	0.831640952198	-0.687232688412	1.33983371419	-12.5734155745	-65.5562761694	7.80719393679
53	1.35554745178	0.728475224521	-1.55651707001	0.406338951398	-1.14085577976	6.81896005584	-0.173649278479	-1.14528184275	0.642721358063	1.05455910042	-1.08871303126	-0.134313953851	-1.27109326822	0.736433196347	1.27580827261	1.38967745439	-0.347098668518	-0.17949794766	1.20914262904	-0.0345190139555	1.30375834539	6.46080405943	-57.9589240591	19.3967565343
54	3.1059274675	-3.66952584606	-0.654210347817	6.56265147172	0.0210980551006	5.65155437004	-0.390719878591	-0.546287781477	0.580851807561	0.313617061801	-0.224242599379	-0.0102680951441	-0.522727171614	0.302196128294	0.582406164349	0.960998944693	0.125156325703	-0.230211452048	0.55701914816	-0.182816134618	0.759059173808	0.50822750133	-66.8138329121	8.84156347968
55	1.48916103721	-2.77532103097	-0.689255067901	5.8971404906	0.385903177768	1.51002056815	-0.493829171428	-0.431476036855	0.654292795016	-0.0449914478111	-0.312655525072	-0.208959624379	-1.08822534445	0.032687727964	0.404826535484	0.982943705146	0.0447322485225	-0.356694768305	0.505807718199	-0.198501945781	0.95564449267	-0.547414807721	-64.4665680423	0.691729023725
56	1.37262422047	-2.20545130852	-0.308925356768	3.58244175651	0.376062612215	0.468530424202	-0.273097019049	0.313938391032	0.56680626284	-0.819596428575	-0.57520435619	-0.481791796308	-0.802390617459	0.286985863593	-0.0191411626768	1.54034906683	-0.00944042171101	-0.5049278327	0.185371684736	-0.04257156952	1.25457976378	-3.19135616261	-55.5912605153	-4.31949142431
57	1.09889623355	-1.85674219193	-0.401466302358	6.25043093667	0.974141992607	0.950735024191	0.0264164060251	0.402619042105	0.92445850986	-1.45373086824	-0.19881017454	-0.0672218587886	-0.53431672477	-0.150174820632	0.169785069112	1.75786177149	0.158512236456	-0.149042878201	0.716090340469	-0.041413676505	1.62673972471	-8.72389151795	-42.8409689838	-9.8526378289
58	4.48168408473	0.237619739836	1.16618129197	1.10322466965	-0.0471832695423	0.424559360951	0.985931569866	0.198185939547	-0.962162382417	-0.185721381515	-0.512936504094	0.572713815259	0.56044931313	-2.23681546661	-0.394972747716	0.816798313381	-0.123142827688	-0.174252636942	1.8536115053	-0.719720691562	2.04561868753	-33.2506410631	-59.5077407985	27.2145794191
59	1.35073727941	-0.549418335697	-0.817068420013	1.53759699839	-0.117446899784	0.652005918396	-0.288188712129	-0.883419418751	1.10006145684	-0.0722355165632	-0.287700576341	1.1697792191	-0.120729348689	-0.877364585223	0.269616470702	0.628683788796	-0.0338946678058	-0.113861202063	1.64143379321	-0.578727169589	1.06517001959	-25.1511356756	-57.2650479679	19.4935077031
60	2.35851351487	0.74312259961	2.71903870269	5.64520444146	-3.14404298474	6.09657869639	0.0848622065364	-1.14271439583	1.1835274177	0.297605173132	0.07210686263	1.36636290325	-0.71945581937	-1.27567642585	-0.0118810831199	0.837756346232	0.126139098882	-0.0936997339289	1.3414831999	-0.324845178514	1.48816787923	-30.9999666916	-49.4938239166	20.9899828362
61	0.114000171106	0.20800500313	-0.273426402693	0.436918144746	-0.499982093747	0.606537343437	0.110591179075	0.166027692106	0.267951642662	0.0963051893473	-0.491397434031	0.85007505334	-0.693422759057	-1.32147202061	0.282208084347	0.87047167502	0.409725299963	-0.30436390003	1.45158467245	-1.00937774416	1.88677580278	-14.548308944	-49.2039803018	23.9472274704
62	2.42236345778	0.418672993954	-0.159608065032	3.18924598015	-3.5446829259	8.35711077437	-0.337484385593	-0.133141193375	-0.212368232495	-1.16562965698	-1.20784158209	1.53508453869	2.18402985755	-0.800880037073	1.37536481706	1.46456105795	-0.25268811685	0.00328971870068	0.702378247468	-0.245510601153	1.03116185151	-3.67149663117	-69.9255979866	23.8006129435
63	4.7615325011	-0.00389772230936	-1.1912816112	2.79852698836	-3.01589898822	8.94582383401	0.088063527776	-0.460360387381	0.588588823892	-0.0707273495162	-1.35650462583	1.62544214398	0.0858937210904	-0.495180142441	1.19010632288	0.586439712401	-0.035121583109	-0.0832363080214	0.986402835058	-0.502848941064	1.071235685	-2.12087725875	-58.8691595859	30.9439309136
64	0.0173996820027	-0.00732087389847	0.0398128019051	0.483593709653	-0.500993813189	0.541874835587	-0.162147759568	0.0504230524316	-0.0324939132663	-0.046583234618	-0.0725506077949	0.128216135232	0.198473577434	-0.364972134406	0.0156741752313	0.817922958505	-0.354911483069	-0.42697220502	1.22925743409	-1.51561773094	1.30785058071	-10.6244539403	-58.731077069	33.8931608434
65	1.73034822294	1.05901821659	1.37191496268	1.40517563916	-0.0651188666344	1.97638448269	-0.334307578275	-0.999186141539	0.0911200940698	0.781990456943	-0.289640090122	0.0830405287917	0.515198780247	-1.19992256697	0.351942492216	0.778056840548	-0.152808279291	0.0374803407542	1.64635499221	-0.908720512424	1.44899225342	-17.2142489614	-60.6375364885	40.1543929446

精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -2 through 29 )	A	A	-2 - 29	1 - 32
2	2	chain 'A' and (resid 30 through 226 )	A	A	30 - 226	33 - 229
3	3	chain 'B' and (resid -2 through 24 )	B	C	-2 - 24	1 - 27
4	4	chain 'B' and (resid 25 through 86 )	B	C	25 - 86	28 - 89
5	5	chain 'B' and (resid 87 through 172 )	B	C	87 - 172	90 - 175
6	6	chain 'B' and (resid 173 through 212 )	B	C	173 - 212	176 - 215
7	7	chain 'B' and (resid 213 through 226 )	B	C	213 - 226	216 - 229
8	8	chain 'C' and (resid -2 through 24 )	C	F	-2 - 24	1 - 27
9	9	chain 'C' and (resid 25 through 86 )	C	F	25 - 86	28 - 89
10	10	chain 'C' and (resid 87 through 103 )	C	F	87 - 103	90 - 106
11	11	chain 'C' and (resid 104 through 129 )	C	F	104 - 129	107 - 132
12	12	chain 'C' and (resid 130 through 143 )	C	F	130 - 143	133 - 146
13	13	chain 'C' and (resid 144 through 163 )	C	F	144 - 163	147 - 166
14	14	chain 'C' and (resid 164 through 189 )	C	F	164 - 189	167 - 192
15	15	chain 'C' and (resid 190 through 212 )	C	F	190 - 212	193 - 215
16	16	chain 'C' and (resid 213 through 228 )	C	F	213 - 228	216 - 231
17	17	chain 'D' and (resid -3 through 24 )	D	I	-3 - 24	1 - 28
18	18	chain 'D' and (resid 25 through 47 )	D	I	25 - 47	29 - 51
19	19	chain 'D' and (resid 48 through 86 )	D	I	48 - 86	52 - 90
20	20	chain 'D' and (resid 87 through 103 )	D	I	87 - 103	91 - 107
21	21	chain 'D' and (resid 104 through 117 )	D	I	104 - 117	108 - 121
22	22	chain 'D' and (resid 118 through 129 )	D	I	118 - 129	122 - 133
23	23	chain 'D' and (resid 130 through 163 )	D	I	130 - 163	134 - 167
24	24	chain 'D' and (resid 164 through 189 )	D	I	164 - 189	168 - 185
25	25	chain 'D' and (resid 190 through 204 )	D	I	190 - 204	186 - 200
26	26	chain 'D' and (resid 205 through 225 )	D	I	205 - 225	201 - 221
27	27	chain 'E' and (resid -3 through 86 )	E	J	-3 - 86	1 - 90
28	28	chain 'E' and (resid 87 through 163 )	E	J	87 - 163	91 - 167
29	29	chain 'E' and (resid 164 through 227 )	E	J	164 - 227	168 - 231
30	30	chain 'F' and (resid -3 through 24 )	F	M	-3 - 24	1 - 28
31	31	chain 'F' and (resid 25 through 86 )	F	M	25 - 86	29 - 90
32	32	chain 'F' and (resid 87 through 163 )	F	M	87 - 163	91 - 167
33	33	chain 'F' and (resid 164 through 227 )	F	M	164 - 227	168 - 231
34	34	chain 'G' and (resid -2 through 24 )	G	O	-2 - 24	1 - 27
35	35	chain 'G' and (resid 25 through 60 )	G	O	25 - 60	28 - 63
36	36	chain 'G' and (resid 61 through 103 )	G	O	61 - 103	64 - 106
37	37	chain 'G' and (resid 104 through 117 )	G	O	104 - 117	107 - 120
38	38	chain 'G' and (resid 118 through 129 )	G	O	118 - 129	121 - 132
39	39	chain 'G' and (resid 130 through 170 )	G	O	130 - 170	133 - 173
40	40	chain 'G' and (resid 171 through 196 )	G	O	171 - 196	174 - 186
41	41	chain 'G' and (resid 197 through 225 )	G	O	197 - 225	187 - 206
42	42	chain 'H' and (resid -2 through 24 )	H	P	-2 - 24	1 - 27
43	43	chain 'H' and (resid 25 through 86 )	H	P	25 - 86	28 - 89
44	44	chain 'H' and (resid 87 through 117 )	H	P	87 - 117	90 - 120
45	45	chain 'H' and (resid 118 through 129 )	H	P	118 - 129	121 - 132
46	46	chain 'H' and (resid 130 through 152 )	H	P	130 - 152	133 - 155
47	47	chain 'H' and (resid 153 through 170 )	H	P	153 - 170	156 - 173
48	48	chain 'H' and (resid 171 through 225 )	H	P	171 - 225	174 - 212
49	49	chain 'I' and (resid -1 through 24 )	I	Q	-1 - 24	1 - 26
50	50	chain 'I' and (resid 25 through 46 )	I	Q	25 - 46	27 - 48
51	51	chain 'I' and (resid 47 through 86 )	I	Q	47 - 86	49 - 88
52	52	chain 'I' and (resid 87 through 117 )	I	Q	87 - 117	89 - 119
53	53	chain 'I' and (resid 118 through 129 )	I	Q	118 - 129	120 - 131
54	54	chain 'I' and (resid 130 through 143 )	I	Q	130 - 143	132 - 145
55	55	chain 'I' and (resid 144 through 163 )	I	Q	144 - 163	146 - 165
56	56	chain 'I' and (resid 164 through 204 )	I	Q	164 - 204	166 - 195
57	57	chain 'I' and (resid 205 through 226 )	I	Q	205 - 226	196 - 217
58	58	chain 'J' and (resid 0 through 24 )	J	R	0 - 24	1 - 25
59	59	chain 'J' and (resid 25 through 36 )	J	R	25 - 36	26 - 37
60	60	chain 'J' and (resid 37 through 46 )	J	R	37 - 46	38 - 47
61	61	chain 'J' and (resid 47 through 110 )	J	R	47 - 110	48 - 111
62	62	chain 'J' and (resid 111 through 129 )	J	R	111 - 129	112 - 130
63	63	chain 'J' and (resid 130 through 144 )	J	R	130 - 144	131 - 145
64	64	chain 'J' and (resid 145 through 155 )	J	R	145 - 155	146 - 156
65	65	chain 'J' and (resid 156 through 223 )	J	R	156 - 223	157 - 184

+
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

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+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)

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ムービー

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構造ビューア

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ビューアのログ

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このページ

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このウェブサイト

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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

-
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)