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- PDB-7jq6: The Phi-28 gp11 DNA packaging Motor -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7jq6
タイトルThe Phi-28 gp11 DNA packaging Motor
要素Encapsidation protein
キーワードVIRAL PROTEIN / ATPase / DNA PACKAGING / MOTOR / PHAGE / ASCE FOLD
機能・相同性Podovirus DNA packaging protein / Podovirus DNA encapsidation protein (Gp16) / Encapsidation protein
機能・相同性情報
生物種Lactococcus phage asccphi28 (ファージ)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.9 Å
データ登録者Morais, M.C. / White, M.A. / Dill, E.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095516 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 米国
引用ジャーナル: Nucleic Acids Res. / 年: 2021
タイトル: Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor.
著者: Pajak, J. / Dill, E. / Reyes-Aldrete, E. / White, M.A. / Kelch, B.A. / Jardine, P.J. / Arya, G. / Morais, M.C.
履歴
登録2020年8月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年6月16日Provider: repository / タイプ: Initial release
改定 1.12021年7月14日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Encapsidation protein
B: Encapsidation protein
C: Encapsidation protein
D: Encapsidation protein
E: Encapsidation protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)226,40616
ポリマ－225,3495
非ポリマー1,05711
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: SAXS, In solution Gp11 forms a dimer of the crystallographic pentamer with D5 symmetry
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area19500 Å2
ΔGint-181 kcal/mol
Surface area85880 Å2
手法PISA
単位格子
Length a, b, c (Å)135.000, 135.000, 276.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDモデル要素
11D-308-

ASN

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 9 through 11 or resid 13...
21(chain B and (resid 9 through 11 or resid 13...
31(chain C and (resid 9 through 11 or resid 13...
41(chain D and (resid 9 through 11 or resid 13...
51(chain E and (resid 9 through 11 or resid 13...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 11 or resid 13...A9 - 11
121(chain A and (resid 9 through 11 or resid 13...A13 - 27
131(chain A and (resid 9 through 11 or resid 13...A29 - 65
141(chain A and (resid 9 through 11 or resid 13...A66
151(chain A and (resid 9 through 11 or resid 13...A5 - 371
161(chain A and (resid 9 through 11 or resid 13...A5 - 371
171(chain A and (resid 9 through 11 or resid 13...A5 - 371
181(chain A and (resid 9 through 11 or resid 13...A5 - 371
191(chain A and (resid 9 through 11 or resid 13...A5 - 371
211(chain B and (resid 9 through 11 or resid 13...B9 - 11
221(chain B and (resid 9 through 11 or resid 13...B13 - 27
231(chain B and (resid 9 through 11 or resid 13...B29 - 65
241(chain B and (resid 9 through 11 or resid 13...B66
251(chain B and (resid 9 through 11 or resid 13...B5 - 370
261(chain B and (resid 9 through 11 or resid 13...B5 - 370
271(chain B and (resid 9 through 11 or resid 13...B5 - 370
281(chain B and (resid 9 through 11 or resid 13...B5 - 370
291(chain B and (resid 9 through 11 or resid 13...B5 - 370
311(chain C and (resid 9 through 11 or resid 13...C9 - 11
321(chain C and (resid 9 through 11 or resid 13...C13 - 27
331(chain C and (resid 9 through 11 or resid 13...C29 - 66
341(chain C and (resid 9 through 11 or resid 13...C68 - 106
351(chain C and (resid 9 through 11 or resid 13...C108 - 130
361(chain C and (resid 9 through 11 or resid 13...C137 - 161
371(chain C and (resid 9 through 11 or resid 13...C0
381(chain C and (resid 9 through 11 or resid 13...C179 - 215
391(chain C and (resid 9 through 11 or resid 13...C280300
3101(chain C and (resid 9 through 11 or resid 13...C300 - 320
3111(chain C and (resid 9 through 11 or resid 13...C322 - 326
3121(chain C and (resid 9 through 11 or resid 13...C322 - 326
3131(chain C and (resid 9 through 11 or resid 13...C328 - 329
3141(chain C and (resid 9 through 11 or resid 13...C331
3151(chain C and (resid 9 through 11 or resid 13...C333 - 344
411(chain D and (resid 9 through 11 or resid 13...D9 - 11
421(chain D and (resid 9 through 11 or resid 13...D13 - 27
431(chain D and (resid 9 through 11 or resid 13...D29 - 65
441(chain D and (resid 9 through 11 or resid 13...D66
451(chain D and (resid 9 through 11 or resid 13...D5 - 372
461(chain D and (resid 9 through 11 or resid 13...D5 - 372
471(chain D and (resid 9 through 11 or resid 13...D5 - 372
481(chain D and (resid 9 through 11 or resid 13...D5 - 372
491(chain D and (resid 9 through 11 or resid 13...D5 - 372
511(chain E and (resid 9 through 11 or resid 13...E9 - 11
521(chain E and (resid 9 through 11 or resid 13...E13 - 27
531(chain E and (resid 9 through 11 or resid 13...E29 - 65
541(chain E and (resid 9 through 11 or resid 13...E66
551(chain E and (resid 9 through 11 or resid 13...E5 - 368
561(chain E and (resid 9 through 11 or resid 13...E5 - 368
571(chain E and (resid 9 through 11 or resid 13...E5 - 368
581(chain E and (resid 9 through 11 or resid 13...E5 - 368
591(chain E and (resid 9 through 11 or resid 13...E5 - 368

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要素

#1: タンパク質
Encapsidation protein


分子量: 45069.855 Da / 分子数: 5 / 由来タイプ: 組換発現
由来: (組換発現) Lactococcus phage asccphi28 (ファージ)
プラスミド: pjExpress401 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B1ABI1
#2: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 11 / 由来タイプ: 合成 / 式: SO4
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.26 Å3/Da / 溶媒含有率: 62.35 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.7
詳細: 1.6 M ammonium sulfate, 0.1 M trisodium citrate, pH 5.7

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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: 2017年10月15日
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: 2.8→50 Å / Num. obs: 82234 / % possible obs: 85.2 % / 冗長度: 42.7 % / Biso Wilson estimate: 62.47 Å2 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.028 / Χ2: 0.994 / Net I/σ(I): 16.9
反射 シェル解像度: 2.8→2.85 Å / 冗長度: 12.3 % / Mean I/σ(I) obs: 0.495 / Num. unique obs: 1138 / CC1/2: 0.518 / CC star: 0.826 / Rpim(I) all: 1.45 / Χ2: 0.904 / % possible all: 31.8

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位相決定

位相決定手法: 単波長異常分散

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解析

ソフトウェア
名称バージョン分類
HKL-2000データスケーリング
SHELX位相決定
PHENIX1.13rc2_2986精密化
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.9→49.3823 Å / SU ML: 0.35 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.72 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2741 3667 4.58 %Random
Rwork0.2412 76360 --
obs0.2427 80027 64.02 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 262.87 Å2 / Biso mean: 101.5328 Å2 / Biso min: 16.01 Å2
精密化ステップサイクル: final / 解像度: 2.9→49.3823 Å
タンパク質核酸リガンド溶媒全体
原子数15397 0 55 0 15452
Biso mean--101.54 --
残基数----1829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7722X-RAY DIFFRACTION7.96TORSIONAL
12B7722X-RAY DIFFRACTION7.96TORSIONAL
13C7722X-RAY DIFFRACTION7.96TORSIONAL
14D7722X-RAY DIFFRACTION7.96TORSIONAL
15E7722X-RAY DIFFRACTION7.96TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.93810.249830.4194351
2.9381-2.97830.337950.34541223
2.9783-3.02080.4963130.36682215
3.0208-3.06590.5804120.41683237
3.0659-3.11380.4998160.396145210
3.1138-3.16490.368290.37754712
3.1649-3.21940.3418340.360972516
3.2194-3.2780.4492520.364197522
3.278-3.3410.3706630.3444127328
3.341-3.40920.3681900.3511179539
3.4092-3.48330.32841150.34249854
3.4833-3.56430.3631680.3332364080
3.5643-3.65340.36962130.3165442695
3.6534-3.75210.28972220.3011451699
3.7521-3.86250.29612280.283453999
3.8625-3.98710.30552120.2683450899
3.9871-4.12960.27492230.2513454599
4.1296-4.29480.31192160.2305456599
4.2948-4.49020.26232200.2132458899
4.4902-4.72670.22062220.18894512100
4.7267-5.02260.22222200.19974627100
5.0226-5.410.2252180.21284608100
5.41-5.95360.29732110.22964566100
5.9536-6.81310.29932200.23884579100
6.8131-8.57650.23432170.22224600100
8.5765-49.38230.21992250.18314575100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.09930.05390.05950.1520.0940.1821-0.00340.16670.0186-0.06910.2012-0.024-0.14670.16460.47170.4074-0.10570.06120.2753-0.10110.273673.962723.617161.1533
20.0572-0.0037-0.04890.0106-0.0150.07460.00470.0313-0.0192-0.00920.00980.00450.0390.00770.02260.409-0.01250.00860.2957-0.15330.196774.882628.595956.2706
30.0476-0.0041-0.03290.00060.00280.02310.0212-0.0097-0.06660.01580.06130.04580.02860.00930.18320.82260.5324-0.16650.76150.18031.121522.474350.333747.8503
40.2814-0.0479-0.05270.00820.00860.01140.0280.0478-0.12330.0133-0.01710.015-0.1016-0.0953-0.09031.31760.8905-0.03941.010.05550.513132.293450.912935.7765
50.01790.01360.01790.01060.01180.01920.00340.00570.02060.08150.0430.06-0.03330.01870.11861.36530.7386-0.0681.01310.17920.865533.472861.691324.418
60.0636-0.03780.01490.0912-0.05740.11570.038-0.0136-0.0658-0.03060.00290.0382-0.1219-0.02530.04271.22410.6348-0.09780.97070.21820.715443.949752.272336.5997
70.136-0.19920.01180.3092-0.04240.03940.04150.015-0.0735-0.0941-0.01950.1943-0.1592-0.1070.03380.8410.5464-0.01460.8260.02210.390439.625947.881545.4918
8-000.00010.0003-00.00080.00570.0359-0.0120.0085-0.0327-0.00110.0235-0.0064-01.5785-0.3304-0.32471.54340.10881.643833.816327.658939.6492
90.0108-0.00650.02790.004-0.01570.0720.01870.0092-0.02580.0521-0.0181-0.1214-0.0939-0.0326-0.00740.76880.4824-0.13660.59880.08370.706342.038241.301452.1742
100.3420.03420.00810.09240.03310.01220.0972-0.0166-0.3505-0.0494-0.03410.0932-0.0759-0.0699-0.08560.91360.6312-0.01460.96340.150.726626.558942.655353.4075
110.0058-0.00240.00370.00260.00380.01640.0077-0.0136-0.0322-0.0095-0.03670.0035-0.0041-0.0091-0.00021.37820.3871-0.16311.6551-0.20441.581911.412738.019436.5275
120.0675-0.00570.00980.0222-0.02110.15810.00090.05710.0961-0.0147-0.0670.0434-0.0042-0.0233-0.02640.68480.41160.31031.63340.42651.230115.760529.26427.0708
130.0694-0.0055-0.04760.02660.01220.03790.01630.1629-0.0083-0.0136-0.11850.1342-0.0865-0.0995-0.22860.75620.48380.04210.9240.17250.965429.693126.723863.7354
140.0143-0.0079-0.00410.02340.00580.0366-0.1476-0.02080.00770.0812-0.0491-0.0492-0.0909-0.0682-0.01850.79790.36910.16040.81840.17950.911632.700819.031172.5062
150.03140.04130.02920.05940.06260.20220.0697-0.0668-0.0294-0.01160.2047-0.0291-0.0885-0.02570.02790.95280.26640.05690.61330.2220.718549.166329.320773.3497
160.02750.04020.00250.0602-0.00450.08850.0320.03770.01740.03460.0328-0.0783-0.0138-0.01310.08370.57390.384-0.14010.7790.15780.956836.4724.408761.8107
170.00860.00270.01120.00960.01630.0371-0.01620.02460.00150.0079-0.0006-0.00530.0015-0.00630.00011.18250.2333-0.29971.05890.02051.17943.774226.736654.3224
180.0887-0.0058-0.00380.0876-0.00580.0005-0.04790.0113-0.00830.02640.1190.1024-0.0458-0.01360.05341.21390.3246-0.44211.51510.23280.907421.55229.97465.1395
190.0992-0.0651-0.08960.1376-0.01530.13040.10870.114-0.11040.12290.169-0.0448-0.0671-0.15120.64240.79310.7796-0.0221.26710.24140.63435.553434.157111.3613
200.0766-0.0831-0.08230.11550.09920.09280.07420.0825-0.068-0.03830.12090.1075-0.005-0.09690.21740.72530.4865-0.12251.29950.02530.663941.676644.11610.204
210.02550.0467-0.01290.086-0.02320.0068-0.01780.09310.0530.03510.10830.0284-0.009-0.01590.03710.80470.5413-0.07371.31850.01750.431541.178650.31244.4271
220.0326-0.0233-0.00950.0315-0.03060.06660.02030.05330.018-0.0071-0.0623-0.06420.01640.0183-0.09060.73110.5190.02290.78520.11550.362637.260541.22821.8448
230.3619-0.05210.02440.1305-0.0010.01350.05370.0253-0.14980.0118-0.0161-0.0654-0.0249-0.0302-0.05420.75360.6190.06581.01520.19360.54133.399228.0816.9445
240.0018-0.0007-0.0035-0.0011-0.00030.00390.0733-0.0020.00980.21640.17680.0672-0.0186-0.11550.11490.80530.5040.14821.02950.32050.642229.020129.505825.7321
250.00280.0058-0.01130.0227-0.03910.06530.0958-0.0197-0.20230.04490.12510.1547-0.0085-0.15640.18930.71670.4713-0.10321.34820.13730.713923.235119.515513.5364
260.00840.00890.00750.02380.010.00710.0005-0.00890.0253-0.0144-0.0612-0.0277-0.01030.0218-0.08580.5988-0.0968-0.35940.71380.25040.672736.326815.6006-6.7113
270.05490.0371-0.01390.05430.0090.01530.0078-0.0484-0.0210.0061-0.01590.0350.0237-0.0507-0.04880.3921-0.278-0.13630.45940.0520.429547.78811.2129-4.5714
280.00370.02190.00940.10720.05020.0223-0.0474-0.12420.0063-0.25590.10820.1565-0.1018-0.190.00580.57560.1128-0.00031.40830.14131.085120.78867.116126.1989
290.02820.02290.04850.03310.04490.08830.1017-0.16450.06080.0024-0.02210.04380.0085-0.12910.02540.40080.1942-0.02431.33880.12820.929616.74233.573737.4617
300.002-0.00040.00140.0052-0.00620.0072-0.0039-0.00570.0023-0.01330.01550.0182-0.03890.002301.05520.3066-0.12791.42030.41341.414919.624415.075646.7256
310.0058-0.013-0.01770.02580.03510.0493-0.02150.07860.0995-0.01660.1189-0.0041-0.1078-0.16680.09410.81290.3373-0.21641.26850.29111.14724.69057.986230.4867
320.0459-0.00640.00460.0124-0.0010.00040.0010.0053-0.0082-0.0075-0.0276-0.0084-0.0086-0.0150.00011.48280.026-0.2521.44090.01411.440333.627915.540635.1563
330.4103-0.23460.03850.1906-0.08490.0873-0.1129-0.09420.16550.09690.0509-0.1662-0.12440.0303-0.13730.2038-0.0341-0.05580.18360.11810.225965.572625.5575-3.7751
340.07790.00990.01710.0042-0.0050.0132-0.06390.02190.05030.04390.012-0.0404-0.06790.0301-0.2320.1867-0.0045-0.10710.2454-0.04710.224471.386641.3513-2.8832
350.0475-0.0513-0.00330.08690.04080.0422-0.1557-0.04540.16670.00530.06960.0931-0.1005-0.0217-0.12040.27720.03180.06070.32390.08150.345164.14744.3609-2.3521
360.21580.00530.05020.10460.10610.2007-0.12220.00010.09470.01070.00280.0286-0.02950.0484-0.56250.05570.0023-0.00610.23370.07290.1856.548729.49952.2352
370.12050.05940.02530.04490.00620.01020.0496-0.03690.05010.13930.05410.23450.014-0.14950.21610.3075-0.04210.07050.36350.16610.358157.403216.13698.8519
380.1188-0.0084-0.05340.0884-0.02470.0692-0.08050.0902-0.02580.03370.0980.06710.0563-0.02630.21460.12360.06170.04850.2060.09380.323662.518912.5422-2.7064
390.0236-0.00720.01440.0184-0.03090.05460.04850.0487-0.0447-0.05740.0103-0.0260.03540.01970.05410.28330.09150.13240.21590.03250.422964.639210.0691-9.4623
400.00450.0013-0.00320.0014-0.00090.00210.0477-0.0699-0.031-0.04210.08360.11280.05240.07990.00010.6471-0.09260.05770.6788-0.11920.77385.709416.6867-1.1797
410.0187-0.01720.02430.0447-0.02380.03060.0060.10270.0201-0.0352-0.0238-0.04770.01050.07020.02820.4365-0.04740.17630.40230.00540.458389.800919.756611.1137
420.0820.0107-0.01970.0649-0.00330.0019-0.00830.1143-0.07-0.09960.22430.07690.1396-0.16520.25440.443-0.016-0.10610.67340.07180.398658.4143-5.2695.7401
430.07990.0493-0.04020.0286-0.02340.0228-0.15590.11010.0032-0.09280.0705-0.10050.1235-0.048-0.02650.538-0.0839-0.08920.39940.11910.424455.1639-13.63849.4964
440.0267-0.0025-0.00340.0352-0.00830.0921-0.05170.07930.0414-0.0055-0.0402-0.0026-0.0168-0.0072-0.04310.3241-0.0106-0.02170.56120.26741.029238.0247-5.60398.9657
450.017-0.00680.01340.0124-0.00240.0108-0.0114-0.0226-0.0165-0.0056-0.05530.0230.012-0.0122-0.00130.72320.20530.15870.8835-0.03861.02444.70490.497419.6154
460.024-0.0236-0.00780.04680.01180.1006-0.0323-0.00290.14580.035-0.0370.0641-0.0111-0.0868-0.08720.42990.04170.03320.27510.02810.403558.1595-2.71079.69
470.00660.00170.00910.00290.00370.01490.0239-0.00690.00750.0022-0.0584-0.0015-0.01410.00350.00010.8151-0.05070.0030.57390.22130.733954.05377.131216.3732
480.00030.0050.00490.03570.0220.0355-0.035-0.0128-0.01570.0196-0.0453-0.1489-0.01760.0595-0.05580.7546-0.3203-0.15090.59360.25440.783896.579841.431325.3635
490.13220.0914-00.07150.0013-0.0005-0.11650.06690.0402-0.0503-0.0153-0.1342-0.25720.1054-0.22490.5191-0.2724-0.1260.160.15240.244784.71639.744322.1924
500.0477-0.05830.06010.0735-0.07380.0806-0.2220.0137-0.00460.17620.05590.0748-0.07170.0609-0.37530.766-0.1178-0.12620.23610.11390.54279.503452.247324.7346
510.03930.01130.03090.01650.05770.2295-0.0152-0.00790.0189-0.0182-0.0290.0062-0.25870.04960.21440.5254-0.1228-0.30330.1173-0.0150.300774.070948.61317.1526
520.0026-0.0011-0.00910.0010.00160.03980.0355-0.0167-0.0123-0.00130.00330.03390.0004-0.00190.00010.67850.1341-0.04750.69840.05580.882871.637824.851213.3105
530.0158-0.0069-0.01650.00250.00520.0168-0.0063-0.0190.090.0174-0.01750.0235-0.0022-0.0283-0.00270.4335-0.2045-0.06120.33280.01280.333980.513932.734821.7043
540.05210.0596-0.03890.1066-0.00310.0691-0.0017-0.0241-0.1037-0.0478-0.0129-0.0541-0.00780.0037-0.18050.3516-0.194-0.10810.19450.15920.325784.637725.937422.2788
550.044-0.04710.02160.07920.0090.04560.0036-0.0084-0.00280.00680.0382-0.03680.02160.01690.04280.5156-0.1348-0.31310.6985-0.03210.5583100.369525.672436.6519
560.13750.0127-0.05910.00250.00140.0618-0.04220.0886-0.13690.0141-0.0024-0.0434-0.04590.0514-0.08890.3333-0.2221-0.22270.48740.13430.585598.154531.067428.2233
570.05170.0208-0.01240.12620.070.0583-0.0840.07380.1164-0.01540.0295-0.0609-0.04090.0718-0.01030.6644-0.18230.08290.42830.11530.604586.234243.842652.4663
580.06850.0897-0.11540.2279-0.19260.2042-0.1099-0.0976-0.0456-0.1816-0.0272-0.1695-0.05290.2689-0.07890.2621-0.0279-0.05480.3374-0.01410.397591.869310.298932.0467
590.04690.04630.03030.060.03360.04880.0158-0.041-0.06-0.01520.0368-0.0687-0.01470.04630.10410.2016-0.08780.04080.44080.11540.495292.3796-1.818732.3057
600.0181-0.0285-0.01940.08740.08410.09190.07910.081-0.0134-0.04280.09250.02280.0598-0.07150.15780.72520.1735-0.03250.37350.14160.465784.4039-3.134915.21
610.00680.0017-0.00070.0003-0.00080.00360.0461-0.02710.0573-0.0427-0.06080.01640.00930.0166-00.3859-0.1184-0.15220.5010.0350.550475.56221.907424.8525
620.0087-0.003-0.00480.0167-0.03250.0679-0.10220.0261-0.0318-0.0111-0.05420.0295-0.04720.0416-0.42370.3033-0.1461-0.08630.34780.08520.538786.70719.5330.7895
630.0882-0.0254-0.00770.09790.0460.0226-0.01020.06870.0445-0.13490.04610.0372-0.1339-0.01940.0010.8444-0.07090.00650.21840.11320.302666.668659.07954.1223
640.20410.0342-0.1680.4421-0.22550.2260.21930.059-0.1-0.04450.10.16120.034-0.22980.67041.04430.1479-0.2160.3830.04050.294357.8555.865245.3336
65-0.0007-0.01240.00370.1295-0.0520.0211-0.1210.14630.1771-0.05240-0.0115-0.19460.0053-0.35371.39120.0301-0.15390.43910.25290.454860.675961.447537.0282
660.0317-0.05160.04060.0839-0.0650.0502-0.02790.05710.0283-0.0097-0.1122-0.1013-0.10790.0855-0.21470.9894-0.1170.09750.46040.07220.36969.926349.508845.0189
670.00430.00290.0040.00350.00180.00360.00360.0798-0.0567-0.02860.0120.01330.03760.0129-01.03620.04950.14371.125-0.16710.817756.045234.688252.2205
680.1404-0.12040.07030.1043-0.05940.05310.05260.16050.0761-0.1132-0.1257-0.10870.04830.0284-0.12780.7708-0.20740.09860.46380.07830.272876.120346.303347.5857
690.02280.0255-0.01180.0291-0.00880.0135-0.03160.0151-0.0089-0.03780.04430.04790.0393-0.0651-0.2320.5921-0.11810.17840.06090.20040.121767.41442.197664.0353
700.1218-0.06460.05810.0669-0.00840.04290.0439-0.04880.0092-0.00010.08150.0256-0.0146-0.11660.35580.5293-0.01080.07940.31650.08290.202972.160950.344564.8377
710.0075-0.00040.00170.00350.00380.0044-0.00680.0060.00870.0285-0.0401-0.012-0.06230.00150.00011.40280.20950.00951.3813-0.2231.376245.464554.093867.7666
720.08690.05280.01540.03210.00890.00260.0911-0.06190.01710.0072-0.0311-0.0222-0.0564-0.05270.0051.66160.62590.19180.88170.09070.527938.459446.380562.5883
730.13820.03730.12030.56480.19690.31240.03650.07670.0391-0.13710.1029-0.14650.03290.09680.38930.3434-0.0799-0.0010.15040.00920.184774.560828.971267.0312
740.01270.00440.02660.00480.01870.2239-0.01340.0103-0.0441-0.0440.0464-0.0241-0.07280.08560.20530.3912-0.00450.09190.18530.02140.435981.671818.9268.4707
750.00340.00170.00240.0011-0.00060.00970.0349-0.00940.07440.05520.0149-0.1204-0.0399-0.0205-00.7737-0.0925-0.0410.74990.17420.70191.766320.527452.6384
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 327:357)B327 - 357
2X-RAY DIFFRACTION2(chain B and resid 358:367)B358 - 367
3X-RAY DIFFRACTION3(chain C and resid 7:27)C7 - 27
4X-RAY DIFFRACTION4(chain C and resid 28:79)C28 - 79
5X-RAY DIFFRACTION5(chain C and resid 80:105)C80 - 105
6X-RAY DIFFRACTION6(chain C and resid 106:131)C106 - 131
7X-RAY DIFFRACTION7(chain C and resid 132:151)C132 - 151
8X-RAY DIFFRACTION8(chain C and resid 152:157)C152 - 157
9X-RAY DIFFRACTION9(chain C and resid 158:176)C158 - 176
10X-RAY DIFFRACTION10(chain C and resid 177:225)C177 - 225
11X-RAY DIFFRACTION11(chain C and resid 226:231)C226 - 231
12X-RAY DIFFRACTION12(chain C and resid 232:251)C232 - 251
13X-RAY DIFFRACTION13(chain C and resid 252:282)C252 - 282
14X-RAY DIFFRACTION14(chain C and resid 283:307)C283 - 307
15X-RAY DIFFRACTION15(chain C and resid 308:327)C308 - 327
16X-RAY DIFFRACTION16(chain C and resid 328:364)C328 - 364
17X-RAY DIFFRACTION17(chain C and resid 365:368)C365 - 368
18X-RAY DIFFRACTION18(chain D and resid 8:20)D8 - 20
19X-RAY DIFFRACTION19(chain D and resid 21:72)D21 - 72
20X-RAY DIFFRACTION20(chain D and resid 73:93)D73 - 93
21X-RAY DIFFRACTION21(chain D and resid 94:108)D94 - 108
22X-RAY DIFFRACTION22(chain D and resid 109:137)D109 - 137
23X-RAY DIFFRACTION23(chain D and resid 138:154)D138 - 154
24X-RAY DIFFRACTION24(chain D and resid 155:181)D155 - 181
25X-RAY DIFFRACTION25(chain D and resid 182:225)D182 - 225
26X-RAY DIFFRACTION26(chain D and resid 226:233)D226 - 233
27X-RAY DIFFRACTION27(chain D and resid 234:251)D234 - 251
28X-RAY DIFFRACTION28(chain D and resid 252:283)D252 - 283
29X-RAY DIFFRACTION29(chain D and resid 284:317)D284 - 317
30X-RAY DIFFRACTION30(chain D and resid 318:331)D318 - 331
31X-RAY DIFFRACTION31(chain D and resid 332:364)D332 - 364
32X-RAY DIFFRACTION32(chain D and resid 365:368)D365 - 368
33X-RAY DIFFRACTION33(chain E and resid 8:65)E8 - 65
34X-RAY DIFFRACTION34(chain E and resid 66:94)E66 - 94
35X-RAY DIFFRACTION35(chain E and resid 95:112)E95 - 112
36X-RAY DIFFRACTION36(chain E and resid 113:151)E113 - 151
37X-RAY DIFFRACTION37(chain E and resid 152:175)E152 - 175
38X-RAY DIFFRACTION38(chain E and resid 176:212)E176 - 212
39X-RAY DIFFRACTION39(chain E and resid 213:224)E213 - 224
40X-RAY DIFFRACTION40(chain E and resid 225:232)E225 - 232
41X-RAY DIFFRACTION41(chain E and resid 233:253)E233 - 253
42X-RAY DIFFRACTION42(chain E and resid 254:281)E254 - 281
43X-RAY DIFFRACTION43(chain E and resid 282:305)E282 - 305
44X-RAY DIFFRACTION44(chain E and resid 306:325)E306 - 325
45X-RAY DIFFRACTION45(chain E and resid 326:334)E326 - 334
46X-RAY DIFFRACTION46(chain E and resid 335:363)E335 - 363
47X-RAY DIFFRACTION47(chain E and resid 364:368)E364 - 368
48X-RAY DIFFRACTION48(chain A and resid 5:19)A5 - 19
49X-RAY DIFFRACTION49(chain A and resid 20:60)A20 - 60
50X-RAY DIFFRACTION50(chain A and resid 61:89)A61 - 89
51X-RAY DIFFRACTION51(chain A and resid 90:128)A90 - 128
52X-RAY DIFFRACTION52(chain A and resid 129:133)A129 - 133
53X-RAY DIFFRACTION53(chain A and resid 134:154)A134 - 154
54X-RAY DIFFRACTION54(chain A and resid 155:205)A155 - 205
55X-RAY DIFFRACTION55(chain A and resid 206:211)A206 - 211
56X-RAY DIFFRACTION56(chain A and resid 212:228)A212 - 228
57X-RAY DIFFRACTION57(chain A and resid 229:250)A229 - 250
58X-RAY DIFFRACTION58(chain A and resid 251:281)A251 - 281
59X-RAY DIFFRACTION59(chain A and resid 282:306)A282 - 306
60X-RAY DIFFRACTION60(chain A and resid 307:325)A307 - 325
61X-RAY DIFFRACTION61(chain A and resid 326:336)A326 - 336
62X-RAY DIFFRACTION62(chain A and resid 337:368)A337 - 368
63X-RAY DIFFRACTION63(chain B and resid 8:51)B8 - 51
64X-RAY DIFFRACTION64(chain B and resid 52:81)B52 - 81
65X-RAY DIFFRACTION65(chain B and resid 82:131)B82 - 131
66X-RAY DIFFRACTION66(chain B and resid 132:151)B132 - 151
67X-RAY DIFFRACTION67(chain B and resid 152:159)B152 - 159
68X-RAY DIFFRACTION68(chain B and resid 160:185)B160 - 185
69X-RAY DIFFRACTION69(chain B and resid 186:212)B186 - 212
70X-RAY DIFFRACTION70(chain B and resid 213:225)B213 - 225
71X-RAY DIFFRACTION71(chain B and resid 226:234)B226 - 234
72X-RAY DIFFRACTION72(chain B and resid 235:251)B235 - 251
73X-RAY DIFFRACTION73(chain B and resid 252:284)B252 - 284
74X-RAY DIFFRACTION74(chain B and resid 285:314)B285 - 314
75X-RAY DIFFRACTION75(chain B and resid 315:326)B315 - 326

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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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