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- PDB-7jqp: 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: 7jqp
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 / 分子置換 / 解像度: 2.89 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11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6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)225,83010
ポリマ－225,3495
非ポリマー4805
水1086
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 area19430 Å2
ΔGint-133 kcal/mol
Surface area80330 Å2
手法PISA
単位格子
Length a, b, c (Å)110.900, 110.900, 351.800
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 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 - 15
131(chain A and (resid 9 through 11 or resid 13...A17 - 62
141(chain A and (resid 9 through 11 or resid 13...A64 - 72
151(chain A and (resid 9 through 11 or resid 13...A74 - 75
161(chain A and (resid 9 through 11 or resid 13...A77 - 86
171(chain A and (resid 9 through 11 or resid 13...A0
181(chain A and (resid 9 through 11 or resid 13...A94 - 956
191(chain A and (resid 9 through 11 or resid 13...A5 - 368
1101(chain A and (resid 9 through 11 or resid 13...A5 - 368
1111(chain A and (resid 9 through 11 or resid 13...A5 - 368
1121(chain A and (resid 9 through 11 or resid 13...A5 - 368
1131(chain A and (resid 9 through 11 or resid 13...A5 - 368
1141(chain A and (resid 9 through 11 or resid 13...A5 - 368
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 - 15
231(chain B and (resid 9 through 11 or resid 13...B17 - 62
241(chain B and (resid 9 through 11 or resid 13...B64 - 72
251(chain B and (resid 9 through 11 or resid 13...B74 - 75
261(chain B and (resid 9 through 11 or resid 13...B77 - 86
271(chain B and (resid 9 through 11 or resid 13...B0
281(chain B and (resid 9 through 11 or resid 13...B94 - 956
291(chain B and (resid 9 through 11 or resid 13...B8 - 367
2101(chain B and (resid 9 through 11 or resid 13...B8 - 367
2111(chain B and (resid 9 through 11 or resid 13...B8 - 367
2121(chain B and (resid 9 through 11 or resid 13...B8 - 367
2131(chain B and (resid 9 through 11 or resid 13...B8 - 367
2141(chain B and (resid 9 through 11 or resid 13...B8 - 367
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 - 15
331(chain C and (resid 9 through 11 or resid 13...C17 - 62
341(chain C and (resid 9 through 11 or resid 13...C64
351(chain C and (resid 9 through 11 or resid 13...C77 - 86
361(chain C and (resid 9 through 11 or resid 13...C94 - 95
371(chain C and (resid 9 through 11 or resid 13...C97 - 109
381(chain C and (resid 9 through 11 or resid 13...C97 - 109
391(chain C and (resid 9 through 11 or resid 13...C111 - 133
3101(chain C and (resid 9 through 11 or resid 13...C137 - 151
3111(chain C and (resid 9 through 11 or resid 13...C160 - 161
3121(chain C and (resid 9 through 11 or resid 13...C162
3131(chain C and (resid 9 through 11 or resid 13...C7 - 368
3141(chain C and (resid 9 through 11 or resid 13...C7 - 368
3151(chain C and (resid 9 through 11 or resid 13...C7 - 368
3161(chain C and (resid 9 through 11 or resid 13...C7 - 368
3171(chain C and (resid 9 through 11 or resid 13...C7 - 368
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 - 15
431(chain D and (resid 9 through 11 or resid 13...D17 - 62
441(chain D and (resid 9 through 11 or resid 13...D64
451(chain D and (resid 9 through 11 or resid 13...D77 - 86
461(chain D and (resid 9 through 11 or resid 13...D94 - 95
471(chain D and (resid 9 through 11 or resid 13...D97 - 106
481(chain D and (resid 9 through 11 or resid 13...D8 - 368
491(chain D and (resid 9 through 11 or resid 13...D107
4101(chain D and (resid 9 through 11 or resid 13...D8 - 368
4111(chain D and (resid 9 through 11 or resid 13...D8 - 368
4121(chain D and (resid 9 through 11 or resid 13...D8 - 368
4131(chain D and (resid 9 through 11 or resid 13...D8 - 368
4141(chain D and (resid 9 through 11 or resid 13...D8 - 368
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
531(chain E and (resid 9 through 11 or (resid 13...E8 - 368
541(chain E and (resid 9 through 11 or (resid 13...E8 - 368
551(chain E and (resid 9 through 11 or (resid 13...E8 - 368
561(chain E and (resid 9 through 11 or (resid 13...E8 - 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: 5 / 由来タイプ: 合成 / 式: SO4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 6 / 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: 2.43 Å3/Da / 溶媒含有率: 49.28 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.3
詳細: 1.0 M trisodium citrate; 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.3

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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6月7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: 2.89→70 Å / Num. obs: 72712 / % possible obs: 98.9 % / 冗長度: 10.9 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.057 / Rrim(I) all: 0.194 / Χ2: 0.991 / Net I/av σ(I): 11 / Net I/σ(I): 5.8
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 allR split
2.89-2.954.82.1110.622200.3020.6811.0272.3620.77989.8
2.95-35.21.8720.6823580.3070.6850.8752.0780.79595.1
3-3.065.81.374124050.5470.8410.6061.5080.82898.4
3.06-3.126.41.2671.224610.6160.8730.5331.3790.82399.9
3.12-3.197.41.0021.725060.7630.930.391.0770.827100
3.19-3.278.50.8552.324560.8570.9610.3060.9090.828100
3.27-3.3510.20.6553.424750.9160.9780.2130.690.883100
3.35-3.4412.10.5524.724720.9660.9910.1650.5760.88699.9
3.44-3.5413.50.4945.324660.9640.9910.140.5140.888100
3.54-3.6513.50.3985.925120.9750.9940.1130.4140.893100
3.65-3.7813.40.3057.124920.9850.9960.0860.3170.96199.89.28
3.78-3.9413.50.2717.525030.9870.9970.0770.2820.99799.9
3.94-4.1113.40.238.725020.9890.9970.0650.2391.04999.9
4.11-4.3313.30.2039.824950.9880.9970.0580.2111.11699.8
4.33-4.613.10.17810.725080.990.9970.0520.1861.19399.2
4.6-4.9612.90.17111.525320.9860.9960.050.1781.24299.5
4.96-5.46130.1551225360.9910.9980.0450.1621.15999.6
5.46-6.2512.90.14412.325740.9910.9980.0420.151.10899.7
6.25-7.8712.80.12612.826230.990.9970.0370.1311.03799.6
7.87-7010.90.10612.127510.9890.9970.0330.1110.85797.8

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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
Rotation8.05 Å49.59 Å
Translation8.05 Å49.59 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
PHENIX1.18.2_3874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: 2.89→50.13 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.74 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2755 3671 5.07 %Random
Rwork0.2257 68727 --
obs0.2282 72398 77.39 %-
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: 196.67 Å2 / Biso mean: 60.5388 Å2 / Biso min: 16.27 Å2
精密化ステップサイクル: final / 解像度: 2.89→50.13 Å
タンパク質核酸リガンド溶媒全体
原子数15065 0 25 6 15096
Biso mean--94.26 47.15 -
残基数----1808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7477X-RAY DIFFRACTION7.986TORSIONAL
12B7477X-RAY DIFFRACTION7.986TORSIONAL
13C7477X-RAY DIFFRACTION7.986TORSIONAL
14D7477X-RAY DIFFRACTION7.986TORSIONAL
15E7477X-RAY DIFFRACTION7.986TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.930.356160.390832734310
2.93-2.970.4963220.372640142312
2.97-3.010.3114250.388751554015
3.01-3.060.381410.380169073121
3.06-3.110.3691530.3594972102529
3.11-3.160.3812700.35561269133937
3.16-3.210.3431880.31781749183751
3.21-3.270.39931250.32962272239766
3.27-3.330.39771620.29962938310087
3.33-3.40.33981790.29133322350198
3.4-3.480.34121820.280334493631100
3.48-3.560.29121770.276233933570100
3.56-3.640.30631860.250734113597100
3.64-3.740.32761840.229333763560100
3.74-3.850.26181820.222733993581100
3.85-3.980.27741750.218334123587100
3.98-4.120.24171840.20933409359399
4.12-4.280.29161770.19843385356299
4.28-4.480.22121880.18133371355999
4.48-4.720.19681780.17643351352999
4.72-5.010.24111770.18863409358699
5.01-5.40.24881740.19493393356799
5.4-5.940.24661760.206633913567100
5.94-6.80.28671790.2234083587100
6.8-8.560.25241840.22163421360599
8.56-50.130.24291870.19663294348197
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)
10.07810.01520.02630.02210.0310.0412-0.0159-0.1097-0.0230.0404-0.05260.1027-0.0183-0.0752-0.21340.0097-0.0695-0.02090.6731-0.17440.333322.14151.33650.983
20.00510.01110.01960.0669-0.00970.1459-0.1178-0.0363-0.00030.00280.00280.1136-0.01830.00440.0040.26330.0391-0.03140.8792-0.07670.62636.00961.70751.476
30.02570.0084-0.02280.0184-0.00490.0249-0.0132-0.0928-0.0253-0.00250.05980.0972-0.0199-0.0627-0.02190.02880.03170.03870.6236-0.08630.444814.265.78750.248
40.1416-0.03560.06590.0205-0.04570.1184-0.0627-0.12970.07560.0163-0.02820.0048-0.0327-0.1379-0.05680.14740.0132-0.01730.3014-0.19520.418630.28663.00943.291
50.2338-0.07650.24210.1603-0.17830.32560.0874-0.21240.0295-0.00930.04810.08040.0656-0.08770.29730.10030.0015-0.04330.513-0.23470.277130.90352.40142.012
60.2415-0.11140.14120.0536-0.01570.21660.1316-0.3212-0.18590.00360.15410.02890.02460.04660.7766-0.06850.00030.00340.5617-0.19510.435736.62244.74447.22
70.0029-0.00170.00270.00120.00070.00330.0886-0.0702-0.0760.06480.0121-0.0080.1881-0.063800.4167-0.1486-0.02350.72690.03320.35798.72629.8138.04
80.04270.00790.00050.1107-0.07190.04840.07910.05560.1197-0.2417-0.02710.1626-0.07640.0331-00.32050.0442-0.02180.4289-0.10210.333253.96933.0435.406
90.02840.03080.02270.03510.02370.01770.0265-0.0311-0.015-0.02140.0293-0.0719-0.0088-0.01060.02070.56340.11560.34180.6544-0.09670.871165.66949.82835.299
100.00190.00170.00090.00810.00150.0002-0.02630.0033-0.00050.0014-0.00350.0141-0.00850.0152-0.00021.1015-0.00740.12081.0080.09860.938256.53548.65225.611
110.00350.00970.00540.04450.02810.01720.0968-0.05450.0741-0.0968-0.08060.0439-0.0774-0.00590.00090.19650.0522-0.03550.5792-0.03180.349348.69438.34633.73
120.0039-0.00130.00870.0004-0.00330.02130.0007-0.0035-0.018-0.02940.01340.03010.0194-0.00570.00010.57120.09770.11240.7906-0.29270.9044-13.72342.35924.25
130.0463-0.01120.00310.02380.01630.03050.095-0.1253-0.05630.0446-0.12980.0756-0.0003-0.0288-0.0740.0872-0.15450.03510.5252-0.21260.3023-8.53944.1731.02
140.0297-0.06570.05010.1917-0.13210.1097-0.0373-0.02670.23750.103-0.18680.1091-0.12190.0252-0.25340.1688-0.0770.03690.5816-0.22160.4-4.22758.48432.576
150.0372-0.02880.03120.09640.00760.0679-0.0218-0.06870.05790.0762-0.0517-0.0005-0.0447-0.0464-0.04540.2302-0.1496-0.12670.5149-0.12440.14413.57346.01328.81
160.0141-0.031-0.00640.09060.00490.03290.0129-0.1016-0.040.02280.15540.0827-0.0480.0130.06970.1688-0.10030.08440.4585-0.05620.220611.02341.61429.212
170.0748-0.09670.02840.1796-0.06960.04530.11520.0922-0.1931-0.04070.0024-0.00170.10070.03950.04060.1817-0.2965-0.06450.4389-0.30320.2291-1.61333.73322.916
180.00590.02420.00790.08870.02910.0105-0.0051-0.0465-0.04380.0234-0.0520.07540.0331-0.0314-0.2040.3414-0.2383-0.06860.6341-0.26630.5424-8.32550.2823.143
190.047-0.0130.02770.0730.00710.022-0.2114-0.0336-0.090.00440.18170.13480.089-0.1219-0.00280.3137-0.09880.11330.4617-0.0790.278118.55618.34914.905
200.01020.00970.0080.01810.00560.0044-0.0743-0.14260.01370.00960.0075-0.0709-0.003-0.0076-0.00080.4505-0.0379-0.08580.5619-0.12530.410829.04517.93728.924
210.0025-0.02030.00190.1616-0.02240.0054-0.0105-0.00680.12580.1943-0.0979-0.0055-0.03790.0353-0.0420.2668-0.1510.06930.38130.01620.383919.91926.71816.713
220.02140.0106-0.00850.0054-0.00410.0033-0.0060.0082-0.01790.0055-0.0115-0.0126-0.00090.0099-0.01090.2056-0.13680.03270.47480.01950.435119.93132.59422.124
230.0367-0.01680.00510.15490.1120.08770.075-0.09040.0837-0.19450.0044-0.0964-0.1849-0.00980.14460.192-0.0260.03520.347-0.36140.2257-1.18975.5727.525
240.0224-0.0463-0.0280.07610.04570.03570.0383-0.1490.13350.0560.0539-0.0737-0.06650.08040.0780.18790.03170.05160.4525-0.36180.304-1.51180.52620.419
250.01950.03240.00050.06350.00030.0635-0.0144-0.0412-0.00630.0076-0.03270.0046-0.0095-0.0658-0.25110.0924-0.05950.01340.3761-0.28650.1667-2.80765.32413.127
260.16910.0819-0.09180.1225-0.13680.1551-0.0580.0478-0.1140.0646-0.07320.06620.04790.0094-0.2920.0569-0.07930.06980.2794-0.17590.30337.361.3363.988
270.12460.03620.11010.21910.04140.0972-0.0494-0.10130.0619-0.1742-0.11850.20070.0441-0.2263-0.42430.2536-0.0366-0.04840.347-0.27040.1341-1.56967.026-5.219
280.0036-0.0031-0.00230.013-0.00570.0047-0.09480.05130.0167-0.13-0.02840.13980.0057-0.0422-0.00130.55570.0737-0.05320.4242-0.10580.449416.10291.506-6.166
290.05250.01130.01340.0154-0.00760.0150.015-0.0057-0.00730.0080.01270.0196-0.00280.00290.00690.4236-0.191-0.03580.4559-0.13370.569516.93180.942-7.005
300.0405-0.05120.02830.0692-0.03890.02190.02390.0889-0.0414-0.2053-0.12740.0275-0.0347-0.0726-0.03970.436-0.06520.07430.4334-0.10820.19968.75349.918-16.676
310.0221-0.02470.01550.0294-0.00940.02720.17720.1112-0.0439-0.28050.01270.11630.00230.0375-0.00020.4655-0.0094-0.00360.3108-0.06680.39649.96843.445-20.486
320.0197-0.0105-0.01610.00690.0160.0685-0.0396-0.07790.00230.0253-0.01580.00780.058-0.0178-0.05490.5332-0.16130.190.3479-0.19420.29245.9334.849-4.713
330.01110.0041-0.00420.0350.02030.01260.081-0.06640.0643-0.26850.0358-0.20140.00080.0033-00.3541-0.00450.05590.4-0.04010.269611.9850.366-9.59
340.0056-0.00150.00170.00360.00040.0028-0.0367-0.00980.0248-0.0129-0.0221-0.0531-0.02730.032801.0146-0.29280.08750.7061-0.33610.707631.335102.80614.393
350.20380.14530.17040.2330.17820.5657-0.0178-0.19830.1210.0197-0.1650.1665-0.0248-0.059-0.61950.3177-0.21290.14290.502-0.34480.335126.29891.91616.38
360.03190.0050.017-00.00240.00850.0522-0.08950.05050.02610.0217-0.0106-0.01450.00950.1490.5595-0.45570.15681.1342-0.3480.50226.04195.77729.641
370.00260.00240.00450.00470.00430.0055-0.012-0.0366-0.04680.0091-0.02960.0132-0.03110.0826-0.02240.6773-0.24420.33011.2136-0.4170.772918.92393.83437.06
380.1732-0.0059-0.0510.10690.18620.3237-0.0196-0.1692-0.0220.0531-0.24760.18120.0921-0.2973-1.1380.2345-0.18230.19490.5158-0.33860.131421.26684.34413.393
390.11320.08610.01610.0777-0.02160.165-0.0035-0.05670.0097-0.0279-0.0580.0131-0.02960.0458-0.13750.255-0.20940.14410.3569-0.11220.319335.54593.1582.788
400.0065-0.0039-0.01320.00160.00730.0268-0.03670.0398-0.0196-0.0625-0.0223-0.0247-0.0035-0.0149-0.00151.1357-0.10770.01871.2347-0.03081.160750.49598.1920.615
410.0618-0.08250.05980.1284-0.04530.0715-0.0138-0.24630.0957-0.01730.024-0.2601-0.02270.0894-0.03840.3704-0.13120.01850.5497-0.17770.464552.5187.5616.926
420.20660.0091-0.05730.0215-0.02060.0445-0.15960.01780.0236-0.2389-0.09010.077-0.1295-0.0579-0.47770.5791-0.02150.1650.1828-0.19720.417938.7277.568-21.126
430.04940.03010.02920.02710.01620.0183-0.00650.026-0.0039-0.0757-0.02070.0169-0.0408-0.0448-0.00790.6293-0.0560.12310.6314-0.35220.557321.21472.863-20.433
440.0283-0.02790.05420.0292-0.05620.11390.0326-0.11720.0747-0.09390.11060.13570.1216-0.03480.0060.5523-0.17180.10560.2764-0.07060.364736.31974.899-9.347
450.001-0.00260.00550.0122-0.00820.0237-0.0181-0.01650.00630.0338-0.0044-0.00130.00810.0016-0.05730.39730.0238-0.10540.5298-0.32320.425154.09381.2950.617
460.2067-0.0550.20940.0179-0.05420.214-0.12410.01210.14140.0208-0.09490.0255-0.06910.02-0.45670.0795-0.0112-0.19370.5349-0.410.501141.77278.34344.552
470.11510.01180.0155-0.00380.00640.00160.0049-0.04850.21250.0215-0.05130.096-0.0428-0.08010.08050.08930.1254-0.0910.6018-0.39960.616630.90382.4547.207
480.0073-0.0008-0.00690.02190.01950.04180.00310.0705-0.0276-0.1021-0.00820.0408-0.07870.03230.06960.2948-0.048-0.10560.351-0.33110.381545.45177.59530.921
490.04470.02070.03650.00720.01630.02430.02540.08770.0046-0.05990.06420.0454-0.03850.04350.29360.08080.0112-0.1370.3733-0.26160.322856.39477.27635.391
500.01710.01690.00250.03220.00160.0001-0.0271-0.00030.0548-0.00390.0166-0.003-0.03380.04310.0220.1354-0.0904-0.0040.4545-0.21180.377562.49679.94840.015
51-0.00050.00050.00010.019-0.00460.0005-0.0118-0.01880.00050.0163-0.0268-0.01690.0124-0.01080.00020.9112-0.03250.00641.15770.13971.118555.72463.01353.752
520.0188-0.0045-0.01660.02150.00370.02450.07-0.18110.0040.0242-0.0053-0.01230.0153-0.0878-0.01050.2177-0.0111-0.16260.7736-0.19790.61852.14955.37946.799
530.04550.0615-0.05430.2148-0.14890.1068-0.1923-0.0180.03910.0235-0.069-0.1487-0.03120.0185-0.02470.4272-0.06370.02440.5244-0.19340.34771.39570.33713.038
540.010.0078-0.01160.0138-0.01550.02070.0558-0.02160.06970.02180.0065-0.0059-0.0472-0.02160.02120.54970.12810.19120.7804-0.16450.426762.26281.3453.427
550.11470.1842-0.08480.591-0.35230.2260.00630.03110.0326-0.09390.13030.06370.08560.06120.23460.3202-0.05180.0390.5385-0.31070.432460.05769.13916.147
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:81 )A5 - 81
2X-RAY DIFFRACTION2( CHAIN A AND RESID 82:91 )A82 - 91
3X-RAY DIFFRACTION3( CHAIN A AND RESID 92:116 )A92 - 116
4X-RAY DIFFRACTION4( CHAIN A AND RESID 117:133 )A117 - 133
5X-RAY DIFFRACTION5( CHAIN A AND RESID 134:157 )A134 - 157
6X-RAY DIFFRACTION6( CHAIN A AND RESID 158:229 )A158 - 229
7X-RAY DIFFRACTION7( CHAIN A AND RESID 230:250 )A230 - 250
8X-RAY DIFFRACTION8( CHAIN A AND RESID 251:309 )A251 - 309
9X-RAY DIFFRACTION9( CHAIN A AND RESID 310:325 )A310 - 325
10X-RAY DIFFRACTION10( CHAIN A AND RESID 326:335 )A326 - 335
11X-RAY DIFFRACTION11( CHAIN A AND RESID 336:368 )A336 - 368
12X-RAY DIFFRACTION12( CHAIN B AND RESID 8:12 )B8 - 12
13X-RAY DIFFRACTION13( CHAIN B AND RESID 13:50 )B13 - 50
14X-RAY DIFFRACTION14( CHAIN B AND RESID 51:133 )B51 - 133
15X-RAY DIFFRACTION15( CHAIN B AND RESID 134:154 )B134 - 154
16X-RAY DIFFRACTION16( CHAIN B AND RESID 155:178 )B155 - 178
17X-RAY DIFFRACTION17( CHAIN B AND RESID 179:228 )B179 - 228
18X-RAY DIFFRACTION18( CHAIN B AND RESID 229:257 )B229 - 257
19X-RAY DIFFRACTION19( CHAIN B AND RESID 258:303 )B258 - 303
20X-RAY DIFFRACTION20( CHAIN B AND RESID 304:325 )B304 - 325
21X-RAY DIFFRACTION21( CHAIN B AND RESID 326:360 )B326 - 360
22X-RAY DIFFRACTION22( CHAIN B AND RESID 361:367 )B361 - 367
23X-RAY DIFFRACTION23( CHAIN C AND RESID 7:70 )C7 - 70
24X-RAY DIFFRACTION24( CHAIN C AND RESID 71:131 )C71 - 131
25X-RAY DIFFRACTION25( CHAIN C AND RESID 132:147 )C132 - 147
26X-RAY DIFFRACTION26( CHAIN C AND RESID 148:176 )C148 - 176
27X-RAY DIFFRACTION27( CHAIN C AND RESID 177:225 )C177 - 225
28X-RAY DIFFRACTION28( CHAIN C AND RESID 226:246 )C226 - 246
29X-RAY DIFFRACTION29( CHAIN C AND RESID 247:254 )C247 - 254
30X-RAY DIFFRACTION30( CHAIN C AND RESID 255:288 )C255 - 288
31X-RAY DIFFRACTION31( CHAIN C AND RESID 289:307 )C289 - 307
32X-RAY DIFFRACTION32( CHAIN C AND RESID 308:329 )C308 - 329
33X-RAY DIFFRACTION33( CHAIN C AND RESID 330:368 )C330 - 368
34X-RAY DIFFRACTION34( CHAIN D AND RESID 8:16 )D8 - 16
35X-RAY DIFFRACTION35( CHAIN D AND RESID 17:64 )D17 - 64
36X-RAY DIFFRACTION36( CHAIN D AND RESID 65:83 )D65 - 83
37X-RAY DIFFRACTION37( CHAIN D AND RESID 84:103 )D84 - 103
38X-RAY DIFFRACTION38( CHAIN D AND RESID 104:181 )D104 - 181
39X-RAY DIFFRACTION39( CHAIN D AND RESID 182:225 )D182 - 225
40X-RAY DIFFRACTION40( CHAIN D AND RESID 226:233 )D226 - 233
41X-RAY DIFFRACTION41( CHAIN D AND RESID 234:263 )D234 - 263
42X-RAY DIFFRACTION42( CHAIN D AND RESID 264:312 )D264 - 312
43X-RAY DIFFRACTION43( CHAIN D AND RESID 313:325 )D313 - 325
44X-RAY DIFFRACTION44( CHAIN D AND RESID 326:368 )D326 - 368
45X-RAY DIFFRACTION45( CHAIN E AND RESID 8:17 )E8 - 17
46X-RAY DIFFRACTION46( CHAIN E AND RESID 18:76 )E18 - 76
47X-RAY DIFFRACTION47( CHAIN E AND RESID 77:132 )E77 - 132
48X-RAY DIFFRACTION48( CHAIN E AND RESID 133:176 )E133 - 176
49X-RAY DIFFRACTION49( CHAIN E AND RESID 177:211 )E177 - 211
50X-RAY DIFFRACTION50( CHAIN E AND RESID 212:224 )E212 - 224
51X-RAY DIFFRACTION51( CHAIN E AND RESID 225:232 )E225 - 232
52X-RAY DIFFRACTION52( CHAIN E AND RESID 233:261 )E233 - 261
53X-RAY DIFFRACTION53( CHAIN E AND RESID 262:306 )E262 - 306
54X-RAY DIFFRACTION54( CHAIN E AND RESID 307:325 )E307 - 325
55X-RAY DIFFRACTION55( CHAIN E AND RESID 326:368 )E326 - 368

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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