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- PDB-7jq7: 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: 7jq7
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) / IODIDE ION / 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 / 分子置換 / 解像度: 2.895 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
改定 1.22023年10月18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 1.32023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
改定 1.42024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _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

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)242,166138
ポリマ－225,3495
非ポリマー16,817133
水19811
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 area19200 Å2
ΔGint-62 kcal/mol
Surface area81290 Å2
手法PISA
単位格子
Length a, b, c (Å)112.200, 112.200, 354.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
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 12 or (resid 13...
21(chain B and (resid 9 through 11 or (resid 12...
31(chain C and (resid 9 through 11 or (resid 12...
41(chain D and (resid 9 through 27 or resid 29...
51(chain E and (resid 9 through 11 or (resid 12...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 12 or (resid 13...A9 - 12
121(chain A and (resid 9 through 12 or (resid 13...A13
131(chain A and (resid 9 through 12 or (resid 13...A3 - 368
141(chain A and (resid 9 through 12 or (resid 13...A3 - 368
151(chain A and (resid 9 through 12 or (resid 13...A3 - 368
161(chain A and (resid 9 through 12 or (resid 13...A3 - 368
211(chain B and (resid 9 through 11 or (resid 12...B9 - 11
221(chain B and (resid 9 through 11 or (resid 12...B12 - 13
231(chain B and (resid 9 through 11 or (resid 12...B5 - 368
241(chain B and (resid 9 through 11 or (resid 12...B5 - 368
251(chain B and (resid 9 through 11 or (resid 12...B5 - 368
261(chain B and (resid 9 through 11 or (resid 12...B5 - 368
311(chain C and (resid 9 through 11 or (resid 12...C9 - 11
321(chain C and (resid 9 through 11 or (resid 12...C12 - 13
331(chain C and (resid 9 through 11 or (resid 12...C2 - 368
341(chain C and (resid 9 through 11 or (resid 12...C2 - 368
351(chain C and (resid 9 through 11 or (resid 12...C2 - 368
361(chain C and (resid 9 through 11 or (resid 12...C2 - 368
411(chain D and (resid 9 through 27 or resid 29...D9 - 27
421(chain D and (resid 9 through 27 or resid 29...D29 - 66
431(chain D and (resid 9 through 27 or resid 29...D68 - 72
441(chain D and (resid 9 through 27 or resid 29...D74
451(chain D and (resid 9 through 27 or resid 29...D83 - 92
461(chain D and (resid 9 through 27 or resid 29...D97 - 106108
471(chain D and (resid 9 through 27 or resid 29...D5 - 368
481(chain D and (resid 9 through 27 or resid 29...D5 - 368
491(chain D and (resid 9 through 27 or resid 29...D5 - 368
4101(chain D and (resid 9 through 27 or resid 29...D5 - 368
4111(chain D and (resid 9 through 27 or resid 29...D5 - 368
511(chain E and (resid 9 through 11 or (resid 12...E9 - 11
521(chain E and (resid 9 through 11 or (resid 12...E12 - 13
531(chain E and (resid 9 through 11 or (resid 12...E5 - 368
541(chain E and (resid 9 through 11 or (resid 12...E5 - 368
551(chain E and (resid 9 through 11 or (resid 12...E5 - 368
561(chain E and (resid 9 through 11 or (resid 12...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-IOD / IODIDE ION


分子量: 126.904 Da / 分子数: 131 / 由来タイプ: 合成 / 式: I
#3: 化合物 ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 11 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: 2.41 Å3/Da / 溶媒含有率: 48.88 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.1
詳細: 1.0 M trisodium citrate; 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.1

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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-G / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2016年8月17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: 2.895→50 Å / Num. obs: 78650 / % possible obs: 99.9 % / 冗長度: 17.3 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.985 / CC star: 0.705 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.041 / Rrim(I) all: 0.172 / Χ2: 1.034 / Net I/σ(I): 19.2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.895-3.059.22.2122850.330.7050.7612.3320.95399.9
3.05-3.1110.21.7651.3922890.5220.8280.5761.8590.951100
3.11-3.1711.51.4841.8122650.6640.8930.4571.5540.961100
3.17-3.2313.21.2562.3723020.7570.9280.3571.3070.998100
3.23-3.315.61.0883.1823030.8560.9610.2821.1250.981100
3.3-3.3816.90.794.2922900.920.9790.1960.8150.96100
3.38-3.4618.60.6775.5622820.9580.9890.160.6961.004100
3.46-3.5619.80.586.8723090.9690.9920.1320.5950.941100
3.56-3.6619.70.458.823010.9770.9940.1020.4620.97100
3.66-3.7819.80.32312.1223240.9880.9970.0740.3311.005100
3.78-3.9119.80.2814.1323050.9910.9980.0640.2881.011100
3.91-4.0719.80.2231723160.9940.9980.0510.2291.008100
4.07-4.2619.70.18420.323250.9950.9990.0420.1881.0399.8
4.26-4.4819.60.14826.323360.9960.9990.0340.1521.09299.8
4.48-4.7619.50.12530.923310.9970.9990.0290.1291.12799.8
4.76-5.1319.40.11831.923780.9970.9990.0270.1211.1100
5.13-5.6419.40.11132.623630.9970.9990.0260.1141.069100
5.64-6.4619.20.137.823770.9970.9990.0230.1031.193100
6.46-8.1318.80.0814124390.9980.9990.0190.0831.19799.8
8.13-5016.30.04746.726050.9960.9990.0120.0490.95699.4

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation8.13 Å49.68 Å
Translation8.13 Å49.68 Å

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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
PHASER2.7.18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: 分子置換
開始モデル: 7JQ6

7jq6


解像度: 2.895→49.6886 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 30.4 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2837 3690 4.7 %Random
Rwork0.2346 74804 --
obs0.237 78494 81.61 %-
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: 228.58 Å2 / Biso mean: 63.5796 Å2 / Biso min: 5.38 Å2
精密化ステップサイクル: final / 解像度: 2.895→49.6886 Å
タンパク質核酸リガンド溶媒全体
原子数15119 0 141 11 15271
Biso mean--86.82 40.2 -
残基数----1825
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7444X-RAY DIFFRACTION12.216TORSIONAL
12B7444X-RAY DIFFRACTION12.216TORSIONAL
13C7444X-RAY DIFFRACTION12.216TORSIONAL
14D7444X-RAY DIFFRACTION12.216TORSIONAL
15E7444X-RAY DIFFRACTION12.216TORSIONAL
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 (%)
2.8954-2.93350.3567170.39873059
2.9335-2.97370.325190.354942412
2.9737-3.01620.349310.380857016
3.0162-3.06120.5098380.357977822
3.0612-3.1090.3354520.3453105730
3.109-3.160.3936890.3307187354
3.16-3.21450.39521500.3149299784
3.2145-3.27290.3141680.3248339898
3.2729-3.33590.33441700.30053523100
3.3359-3.40390.30531770.27913567100
3.4039-3.47790.35231770.27863500100
3.4779-3.55880.30641770.26483530100
3.5588-3.64780.32031740.25513512100
3.6478-3.74640.29711730.23393556100
3.7464-3.85660.32481750.22393518100
3.8566-3.9810.29821770.223519100
3.981-4.12320.23031710.20853503100
4.1232-4.28820.27071690.20483539100
4.2882-4.48330.23921770.18783531100
4.4833-4.71950.22011720.17963491100
4.7195-5.01490.2451760.19423500100
5.0149-5.40170.28591750.20523518100
5.4017-5.94450.23691770.22263543100
5.9445-6.80280.34971790.2413510100
6.8028-8.56370.28921650.25073527100
8.5637-49.6810.23151650.2142351599
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)
10.03660.002-0.01420.0176-0.00760.0147-0.01770.07960.0722-0.2454-0.07910.01220.02950.11750.00010.4191-0.08880.00840.4666-0.08220.400765.123969.922919.443
20.03340.0146-0.02910.0145-0.00710.02870.05530.0171-0.0228-0.01080.0472-0.00320.0246-0.05370.00250.8135-0.192-0.00020.9573-0.32110.722852.865771.769216.2125
30.11290.01640.06350.01790.0060.03480.0545-0.0375-0.1496-0.01880.05960.14490.00520.03140.02050.41960.02970.19781.0784-0.07440.774624.689743.827856.9691
40.1177-0.0775-0.00350.2169-0.04680.0159-0.25850.0529-0.0042-0.06080.05960.2270.0585-0.0415-0.29170.17610.06210.03190.5087-0.15340.466927.242553.191150.3223
50.06930.0139-0.0683-0.00080.01170.2504-0.1202-0.10680.04510.064-0.08170.3113-0.0477-0.1494-0.17630.1412-0.07950.03880.8221-0.11070.902314.280557.332250.3395
60.1967-0.18710.02790.2302-0.09650.1935-0.0517-0.08530.07510.04290.16860.1325-0.0754-0.2099-0.07730.11860.0442-0.00740.3468-0.11250.589919.619665.42348.9402
70.00550.00340.00010.0079-0.00150.00330.00730.01830.0116-0.04570.0407-0.033-0.02020.0144-0.00010.72350.1806-0.26930.8346-0.22940.680941.518964.890338.5059
80.16030.01270.03590.0678-0.05150.2350.0055-0.06020.0178-0.00960.1230.06180.0256-0.07560.38270.0910.0553-0.00930.4502-0.18230.487432.972354.958144.9057
90.0888-0.03610.00540.025-0.030.08280.051-0.10740.0049-0.00940.06680.1069-0.05630.08180.5242-0.1119-0.04470.05540.3915-0.19510.537539.549749.933144.6805
100.00970.0040.00040.00270.00150.00070.0865-0.0276-0.02110.00650.1019-0.01670.0198-0.0121-0.00010.54190.00210.10580.4762-0.22110.847736.842129.750949.0294
110.0393-0.0220.03190.035-0.02970.0305-0.05590.0035-0.1015-0.01140.07660.21430.26880.0899-0.00180.257-0.0662-0.00770.5086-0.06630.680235.118438.425553.8278
120.0445-0.00260.03610.0121-0.00980.03930.1063-0.0697-0.0315-0.0220.007-0.1442-0.03490.050.13460.15450.02470.10760.49410.00220.390410.392630.73138.8429
130.0778-0.0025-0.00640.1613-0.09430.0719-0.0085-0.1821-0.0461-0.09880.10150.2186-0.04950.17410.12150.26190.0945-0.15130.5267-0.13680.34150.310734.714838.0706
140.16480.0332-0.010.29970.02990.0106-0.0341-0.0506-0.0072-0.0778-0.02140.0344-0.04350.1222-0.11590.1766-0.0108-0.03830.6044-0.14550.165860.813431.60133.2036
150.013-0.01890.00180.01670.00140.0229-0.1703-0.02660.252-0.0023-0.08950.17130.17840.0031-0.00020.3445-0.0479-0.00390.6851-0.16740.551468.120948.639935.0537
160.00170.0035-0.00160.0096-0.00040.00040.07140.05230.1018-0.0175-0.0319-0.0293-0.0354-0.0114-00.53020.094-0.01260.34290.0380.417557.743348.542125.8271
170.08860.035-0.02650.0436-0.00650.0192-0.015-0.02220.185-0.3282-0.15780.1830.0332-0.1622-0.06380.29790.0346-0.01980.4083-0.0690.193750.468238.859134.6143
180.0785-0.0609-0.04020.0510.0340.01860.0516-0.0116-0.0383-0.07390.01810.24160.0007-0.12420.12260.02910.2075-0.01950.5602-0.16860.367-8.216346.042229.619
190.01710.06-0.0240.2271-0.08760.0442-0.02080.08670.0152-0.2619-0.13070.1378-0.0867-0.1857-0.76070.15650.1220.02480.3358-0.26880.1175-2.693857.024827.2608
200.11290.1628-0.11350.3018-0.17910.13370.11870.03810.11190.20330.02770.1212-0.1182-0.06020.07570.19650.1135-0.00080.4457-0.16280.3651-3.552662.036635.8767
210.04670.10170.0090.2167-0.01350.2714-0.0617-0.08950.1597-0.04630.14280.0579-0.05-0.04350.37730.1154-0.03810.01830.4975-0.27160.29125.223747.397232.8341
220.0127-0.01040.00970.0123-0.00360.01380.00490.02310.0442-0.1018-0.0662-0.0241-0.03680.06710.00040.5713-0.13640.24170.8360.06430.662713.08747.509312.1974
230.0024-0.0014-0.01650.04270.13010.47450.0114-0.1153-0.06260.16290.14720.0555-0.11630.18230.16810.2160.03260.19710.4454-0.12380.22217.860541.135435.2329
240.00660.00430.00490.00880.0073-0.0007-0.01670.0691-0.1035-0.08210.0703-0.0050.08680.04430.08350.139-0.08230.09180.3653-0.17520.10973.027233.807518.1889
250.03480.00370.01250.01270.00170.00580.3239-0.0397-0.1010.1073-0.1035-0.1544-0.0729-0.17660.00090.51350.023-0.00580.4805-0.04160.2707-3.684731.817125.1072
26-0.0018-0.00090.0003-0.0006-0.00060.0003-0.0505-0.0627-0.05340.09240.07380.11830.09020.08960.00030.7413-0.1576-0.10210.6617-0.3311.0176-13.976249.22888.0954
270.03730.04590.02950.05370.04660.08920.0156-0.0148-0.0437-0.0283-0.00690.05560.0424-0.0934-0.08270.3015-0.36750.03360.5069-0.27480.5275-5.855254.62990.8625
280.0636-0.00540.01990.0370.04180.0471-0.22970.06430.00730.1140.09130.01270.10460.0183-0.00010.5757-0.010.08970.4634-0.07620.359914.68724.537116.0155
290.0135-0.02770.0260.0428-0.04360.0529-0.06-0.25650.04070.18010.0146-0.1237-0.0819-0.1651-0.110.4039-0.07540.13310.3613-0.11580.117524.193616.677516.2497
300.00660.0090.00520.00810.00450.0059-0.0169-0.011-0.06570.00420.02310.06580.00410.02501.00360.1132-0.21920.6997-0.0560.558931.781822.220432.5047
310.04-0.08730.07470.1727-0.16080.1577-0.01880.0304-0.1739-0.043-0.0896-0.0116-0.14210.0012-0.09450.1826-0.12090.05570.391-0.08060.40721.510227.702915.9146
320.03310.0040.00260.02350.00280.0075-0.0374-0.02110.0620.06250.06780.0736-0.01070.05230.00050.2013-0.0587-0.00620.3857-0.08490.294919.537131.377821.8458
330.0655-0.00440.05220.0585-0.00390.04640.05820.0580.1113-0.1739-0.10160.1046-0.0651-0.1224-0.09880.43820.062-0.0010.3354-0.19240.3909-2.645779.3536-1.8866
340.0277-0.0294-0.05170.04660.05050.22370.0725-0.05530.1267-0.0465-0.05150.0234-0.24230.06010.05570.262-0.07640.07770.2563-0.49060.31691.62679.178312.2972
350.0228-0.0052-0.00730.06320.01010.00470.04830.07220.0184-0.11190.0041-0.0942-0.22590.02130.04790.4068-0.03890.2090.5739-0.36720.3333-2.304289.313323.3057
360.0156-0.01680.01970.03130.00170.07980.0212-0.1489-0.00570.09950.0454-0.01370.05580.07770.09320.2180.00050.05670.3797-0.18820.41882.137171.324720.7
370.02440.0758-0.02650.28370.01630.2185-0.0772-0.0897-0.03420.0353-0.22070.13390.1928-0.1953-0.68410.15130.04340.13230.448-0.14450.12251.074166.832410.6282
380.007-0.00980.00410.0213-0.0070.0054-0.05770.00040.0272-0.0103-0.0063-0.0538-0.01310.0149-00.79540.16750.07340.8446-0.2291.17820.564569.23790.1059
390.19580.001-0.06890.0171-0.01680.1589-0.04-0.0386-0.00080.1119-0.05570.09340.07270.0156-0.5110.2042-0.10240.17320.3303-0.25560.10893.630158.60626.2544
400.08950.00810.10830.16510.08520.1647-0.04580.03970.0699-0.2226-0.1730.26980.0581-0.343-0.4560.3139-0.0486-0.00620.2092-0.35880.1792-0.64668.1904-5.1559
41-0.00050.0013-0.00050.0059-0.00230.0005-0.04930.0326-0.0338-0.0067-0.0061-0.00110.0075-0.0127-0.00011.01220.04480.15130.6775-0.00131.06978.547988.792-10.2136
420.017-0.00540.01020.0039-0.00540.00860.13060.1441-0.0531-0.0260.11040.0087-0.0362-0.00910.00010.7744-0.050.07440.35360.01110.494921.032891.5643-5.2765
430.3325-0.12750.06940.1054-0.0930.09460.01520.32580.16290.0027-0.24140.1829-0.0833-0.1232-0.07310.5285-0.10720.07220.4346-0.0550.27258.789354.5879-15.142
440.0565-0.0088-0.0250.0556-0.0080.02460.1857-0.0725-0.0389-0.2293-0.07110.22630.07690.0656-0.00130.3377-0.0148-0.01860.3822-0.12280.390711.853844.7274-20.9553
450.03690.0045-0.00690.022-0.05540.13770.0248-0.0167-0.06240.07180.0652-0.06840.05090.00120.05360.6021-0.04570.10130.3104-0.07090.18536.303135.412-5.3575
460.14980.0972-0.08320.2592-0.1520.37520.13680.14630.043-0.02060.1213-0.1281-0.130.02170.1110.4349-0.09210.02510.29-0.02050.290312.733351.1104-10.3016
470.0388-0.0550.06080.0793-0.0880.1084-0.1108-0.00590.04930.10160.0262-0.0386-0.0868-0.0088-0.14610.4487-0.1180.00310.5118-0.2840.387714.815751.24090.2611
480.04210.00750.04370.0253-0.01470.0641-0.0824-0.02310.04760.13890.1351-0.12030.04920.04180.14040.925-0.15830.21910.946-0.54760.721332.5076104.100713.3022
490.12170.0676-0.09610.0348-0.03430.0776-0.0081-0.4557-0.05390.03390.0259-0.0492-0.01760.2655-0.03480.4637-0.04440.10740.8981-0.17080.336127.547291.429819.5469
501.0012-0.24690.32330.2537-0.09740.10720.3412-0.0884-0.08760.02410.2718-0.1095-0.1144-0.01750.12220.9758-0.1430.10971.6903-0.35190.62125.677897.766134.0558
510.00070.001-0.00270.0060.00450.00440.05760.13020.06780.06510.0511-0.0109-0.0065-0.0050.00010.7904-0.19780.0971.1531-0.23370.468318.288796.52834.299
520.0849-0.0132-0.02960.0079-0.00250.03130.0628-0.02660.00860.0601-0.12240.08490.10080.08120.06110.5966-0.01660.2470.9756-0.14420.455517.250684.57718.452
530.13610.0499-0.01250.05090.05680.1074-0.0174-0.0488-0.04080.02250.1089-0.0814-0.1906-0.02090.03910.5919-0.18660.28440.625-0.15780.311530.359587.497812.196
540.1004-0.10620.01860.36850.07210.04930.1734-0.2584-0.10750.1288-0.30850.26860.09070.0394-0.00550.4336-0.09720.21470.4480.00550.428324.238884.6745.3924
550.0038-0.0042-0.020.1329-0.05270.1734-0.0126-0.12630.0932-0.14670.0467-0.0406-0.08670.18780.04580.3526-0.28370.30070.5264-0.10740.230636.755694.28472.8907
560.00340.00120.00640.00240.00480.01170.02260.15080.02120.0305-0.03210.0035-0.001-0.06630.00010.7454-0.3213-0.18670.9852-0.05511.026652.767199.372321.0789
570.0084-0.0014-0.00720.0079-0.00890.01470.1158-0.00080.14470.0013-0.0143-0.0153-0.09490.17590.00010.9309-0.4170.07420.9143-0.03740.503357.385389.414925.803
580.1911-0.228-0.16570.28160.22170.18470.0695-0.1766-0.193-0.1169-0.33150.0095-0.11860.1311-0.04160.635-0.10760.1130.40390.02340.370141.487783.6579-11.5902
590.01170.0020.02890.03340.01040.0552-0.1074-0.08260.0558-0.050.12540.0042-0.21370.0995-00.4789-0.00780.06820.3299-0.06670.360838.564777.1701-21.3268
600.0058-0.005-0.00720.01390.00950.0260.00940.0045-0.1025-0.0101-0.0229-0.0476-0.047-0.1556-0.00070.6891-0.04040.14610.4575-0.11270.554125.093270.5553-18.6385
610.1010.0122-0.07540.0018-0.00510.0622-0.1298-0.2062-0.0991-0.0731-0.00360.25920.03830.2566-0.00450.4863-0.07940.04520.3158-0.11350.399939.755778.5421-9.8696
620.0075-0.0040.01240.0032-0.0060.02650.0345-0.0172-0.01980.0519-0.0173-0.02310.0140.0225-0.00020.73840.00450.00080.71720.04320.870632.608271.71-3.1509
630.11090.07470.06130.07630.05560.0451-0.0204-0.0340.02460.06310.07480.1523-0.01330.06830.18890.2118-0.02-0.09640.5207-0.13820.439547.202379.932844.907
640.0938-0.0092-0.01640.1019-0.04070.024-0.1053-0.00730.02810.10630.0720.080.0959-0.07880.01220.1891-0.0367-0.01590.2186-0.11440.498833.600778.745954.8363
650.10970.1742-0.23350.2878-0.38220.51150.12770.10330.26540.04520.31110.3666-0.0391-0.14670.31570.36860.0721-0.12380.5698-0.24620.771830.172184.708650.9523
660.2093-0.1085-0.04670.2614-0.40270.96290.0609-0.00620.01620.02420.28540.0909-0.2189-0.09570.22080.3738-0.0965-0.00640.2919-0.1910.586440.231983.31536.5067
670.0088-0.00190.00940.00990.01750.03430.2428-0.0139-0.0859-0.1490.0670.07930.1342-0.066700.60570.0089-0.15190.3752-0.02250.499649.016775.163227.3062
680.10560.044-0.12440.015-0.05050.14790.01160.11430.116-0.12160.10750.0578-0.26090.0311-0.02150.2756-0.0741-0.0410.341-0.11190.364157.886278.879935.7377
690.0077-0.00180.00370.01250.00330.0024-0.0492-0.00540.0244-0.03420.0289-0.0577-0.12680.0926-00.4129-0.18830.08430.5156-0.07670.328363.711881.390140.1543
700.00080.0058-0.00420.0141-0.01360.0105-0.1289-0.0541-0.03720.0376-0.01210.04970.02670.0636-0.00030.82260.0553-0.13330.9004-0.16490.772657.899363.370554.0688
710.023-0.0139-0.02790.12950.03620.0399-0.0344-0.098-0.1139-0.0370.1397-0.1595-0.02040.04090.04740.1345-0.0574-0.01030.7637-0.23450.41850.758753.328851.3404
720.2864-0.0605-0.14930.1841-0.04170.38390.0503-0.1889-0.073-0.1731-0.03950.0125-0.2749-0.19780.00290.3467-0.15120.01310.3-0.08410.355668.967471.692120.4637
730.0775-0.0268-0.0160.01480.02570.0697-0.0228-0.02050.01980.05580.04130.0158-0.07470.13030.02280.5271-0.13050.10960.4064-0.19720.349773.814869.188912.2098
740.014-0.00750.01140.007-0.00010.0108-0.00130.0671-0.02370.01170.0814-0.0256-0.1623-0.13830.00020.6739-0.03980.160.4843-0.10180.437364.237582.43663.669
750.006-0.0152-0.01870.03910.0550.09090.00990.0534-0.0114-0.04170.0740.0293-0.01430.07360.00330.6793-0.1906-0.04771.38640.24790.824755.323371.81145.543
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and resid 335:363)E335 - 363
2X-RAY DIFFRACTION2(chain E and resid 364:368)E364 - 368
3X-RAY DIFFRACTION3(chain A and resid 1:19)A1 - 19
4X-RAY DIFFRACTION4(chain A and resid 20:60)A20 - 60
5X-RAY DIFFRACTION5(chain A and resid 61:89)A61 - 89
6X-RAY DIFFRACTION6(chain A and resid 90:128)A90 - 128
7X-RAY DIFFRACTION7(chain A and resid 129:133)A129 - 133
8X-RAY DIFFRACTION8(chain A and resid 134:154)A134 - 154
9X-RAY DIFFRACTION9(chain A and resid 155:205)A155 - 205
10X-RAY DIFFRACTION10(chain A and resid 206:211)A206 - 211
11X-RAY DIFFRACTION11(chain A and resid 212:228)A212 - 228
12X-RAY DIFFRACTION12(chain A and resid 229:250)A229 - 250
13X-RAY DIFFRACTION13(chain A and resid 251:281)A251 - 281
14X-RAY DIFFRACTION14(chain A and resid 282:306)A282 - 306
15X-RAY DIFFRACTION15(chain A and resid 307:325)A307 - 325
16X-RAY DIFFRACTION16(chain A and resid 326:336)A326 - 336
17X-RAY DIFFRACTION17(chain A and resid 337:368)A337 - 368
18X-RAY DIFFRACTION18(chain B and resid 1:51)B1 - 51
19X-RAY DIFFRACTION19(chain B and resid 52:81)B52 - 81
20X-RAY DIFFRACTION20(chain B and resid 82:131)B82 - 131
21X-RAY DIFFRACTION21(chain B and resid 132:151)B132 - 151
22X-RAY DIFFRACTION22(chain B and resid 152:159)B152 - 159
23X-RAY DIFFRACTION23(chain B and resid 160:185)B160 - 185
24X-RAY DIFFRACTION24(chain B and resid 186:212)B186 - 212
25X-RAY DIFFRACTION25(chain B and resid 213:225)B213 - 225
26X-RAY DIFFRACTION26(chain B and resid 226:234)B226 - 234
27X-RAY DIFFRACTION27(chain B and resid 235:251)B235 - 251
28X-RAY DIFFRACTION28(chain B and resid 252:284)B252 - 284
29X-RAY DIFFRACTION29(chain B and resid 285:314)B285 - 314
30X-RAY DIFFRACTION30(chain B and resid 315:326)B315 - 326
31X-RAY DIFFRACTION31(chain B and resid 327:357)B327 - 357
32X-RAY DIFFRACTION32(chain B and resid 358:367)B358 - 367
33X-RAY DIFFRACTION33(chain C and resid 1:27)C1 - 27
34X-RAY DIFFRACTION34(chain C and resid 28:79)C28 - 79
35X-RAY DIFFRACTION35(chain C and resid 80:105)C80 - 105
36X-RAY DIFFRACTION36(chain C and resid 106:131)C106 - 131
37X-RAY DIFFRACTION37(chain C and resid 132:151)C132 - 151
38X-RAY DIFFRACTION38(chain C and resid 152:157)C152 - 157
39X-RAY DIFFRACTION39(chain C and resid 158:176)C158 - 176
40X-RAY DIFFRACTION40(chain C and resid 177:225)C177 - 225
41X-RAY DIFFRACTION41(chain C and resid 226:231)C226 - 231
42X-RAY DIFFRACTION42(chain C and resid 232:251)C232 - 251
43X-RAY DIFFRACTION43(chain C and resid 252:282)C252 - 282
44X-RAY DIFFRACTION44(chain C and resid 283:307)C283 - 307
45X-RAY DIFFRACTION45(chain C and resid 308:327)C308 - 327
46X-RAY DIFFRACTION46(chain C and resid 328:364)C328 - 364
47X-RAY DIFFRACTION47(chain C and resid 365:368)C365 - 368
48X-RAY DIFFRACTION48(chain D and resid 1:20)D1 - 20
49X-RAY DIFFRACTION49(chain D and resid 21:72)D21 - 72
50X-RAY DIFFRACTION50(chain D and resid 73:93)D73 - 93
51X-RAY DIFFRACTION51(chain D and resid 94:108)D94 - 108
52X-RAY DIFFRACTION52(chain D and resid 109:137)D109 - 137
53X-RAY DIFFRACTION53(chain D and resid 138:154)D138 - 154
54X-RAY DIFFRACTION54(chain D and resid 155:181)D155 - 181
55X-RAY DIFFRACTION55(chain D and resid 182:225)D182 - 225
56X-RAY DIFFRACTION56(chain D and resid 226:233)D226 - 233
57X-RAY DIFFRACTION57(chain D and resid 234:251)D234 - 251
58X-RAY DIFFRACTION58(chain D and resid 252:283)D252 - 283
59X-RAY DIFFRACTION59(chain D and resid 284:317)D284 - 317
60X-RAY DIFFRACTION60(chain D and resid 318:331)D318 - 331
61X-RAY DIFFRACTION61(chain D and resid 332:364)D332 - 364
62X-RAY DIFFRACTION62(chain D and resid 365:368)D365 - 368
63X-RAY DIFFRACTION63(chain E and resid 1:65)E1 - 65
64X-RAY DIFFRACTION64(chain E and resid 66:94)E66 - 94
65X-RAY DIFFRACTION65(chain E and resid 95:112)E95 - 112
66X-RAY DIFFRACTION66(chain E and resid 113:151)E113 - 151
67X-RAY DIFFRACTION67(chain E and resid 152:175)E152 - 175
68X-RAY DIFFRACTION68(chain E and resid 176:212)E176 - 212
69X-RAY DIFFRACTION69(chain E and resid 213:224)E213 - 224
70X-RAY DIFFRACTION70(chain E and resid 225:232)E225 - 232
71X-RAY DIFFRACTION71(chain E and resid 233:253)E233 - 253
72X-RAY DIFFRACTION72(chain E and resid 254:281)E254 - 281
73X-RAY DIFFRACTION73(chain E and resid 282:305)E282 - 305
74X-RAY DIFFRACTION74(chain E and resid 306:325)E306 - 325
75X-RAY DIFFRACTION75(chain E and resid 326:334)E326 - 334

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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://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