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- PDB-5t2f: Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 5t2f
タイトルStructure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4
要素DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
キーワードCELL CYCLE / FHA / BRCT / protein chimera
機能・相同性
機能・相同性情報


positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / deoxyribonucleoside triphosphate biosynthetic process / positive regulation of nuclear cell cycle DNA replication / positive regulation of meiosis I / meiotic recombination checkpoint signaling / regulation of cell cycle phase transition ...positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / deoxyribonucleoside triphosphate biosynthetic process / positive regulation of nuclear cell cycle DNA replication / positive regulation of meiosis I / meiotic recombination checkpoint signaling / regulation of cell cycle phase transition / premeiotic DNA replication / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / dual-specificity kinase / mitotic DNA replication checkpoint signaling / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / chromosome segregation / intracellular protein localization / protein tyrosine kinase activity / protein kinase activity / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / chromatin / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Serine/threonine-protein kinase Rad53 / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. ...Regulatory subunit Dfp1/Him1, central region / : / Dfp1/Him1, central region / BRCT domain / Serine/threonine-protein kinase Rad53 / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Serine/threonine-protein kinase RAD53 / DDK kinase regulatory subunit DBF4
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.66 Å
データ登録者Guarne, A. / Almawi, A.W. / Matthews, L.A.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)MOP-67189 カナダ
引用ジャーナル: Sci Rep / 年: 2016
タイトル: 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.
著者: Almawi, A.W. / Matthews, L.A. / Myrox, P. / Boulton, S. / Lai, C. / Moraes, T. / Melacini, G. / Ghirlando, R. / Duncker, B.P. / Guarne, A.
履歴
登録2016年8月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年3月15日Provider: repository / タイプ: Initial release
改定 1.12017年3月22日Group: Structure summary
改定 1.22020年1月8日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年10月4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

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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: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
B: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
D: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)124,59018
ポリマ－123,7214
非ポリマー86914
水2,756153
1
A: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,1174
ポリマ－30,9301
非ポリマー1863
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,1174
ポリマ－30,9301
非ポリマー1863
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,1795
ポリマ－30,9301
非ポリマー2484
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,1795
ポリマ－30,9301
非ポリマー2484
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)57.775, 66.527, 86.520
Angle α, β, γ (deg.)109.24, 90.88, 90.30
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein / Dumbbell forming protein 4 / CHEK2 homolog / Serine-protein kinase 1


分子量: 30930.336 Da / 分子数: 4
断片: UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS
由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母), (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c
遺伝子: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588
プラスミド: pET15b
詳細 (発現宿主): includes a 6xHis-SUMO tag removable with TEV protease
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: P32325, UniProt: P22216, dual-specificity kinase
#2: 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: 14 / 由来タイプ: 合成 / 式: C2H6O2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 153 / 由来タイプ: 天然 / 式: H2O

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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: 2.55 Å3/Da / 溶媒含有率: 51.77 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: NSLS / ビームライン: X29A / 波長: 1.1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013年11月25日
放射モノクロメーター: double crystals / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.1 Å / 相対比: 1
反射解像度: 2.3→35 Å / Num. obs: 48005 / % possible obs: 87.2 % / 冗長度: 1.6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.6
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.341.40.1673.20.925157.3
2.34-2.381.40.163.60.935164.6
2.38-2.431.50.1693.50.931170.4
2.43-2.481.50.14540.952175.6
2.48-2.531.60.1374.30.945179.8
2.53-2.591.50.12750.955181.4
2.59-2.661.60.1155.40.964187.1
2.66-2.731.60.116.30.961188.8
2.73-2.811.60.09670.972191.5
2.81-2.91.70.0947.90.976194.8
2.9-31.70.0799.70.981194.8
3-3.121.60.0739.70.981195.8
3.12-3.261.70.06211.40.983195.5
3.26-3.431.70.05312.40.987195.7
3.43-3.651.70.04413.70.991195.8
3.65-3.931.70.03914.10.991195.8
3.93-4.331.70.03616.10.993195.4
4.33-4.951.70.03216.60.992194.6
4.95-6.231.70.0316.60.995195.8
6.23-351

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1G6G, 3QBZ

1g6g

3qbz


解像度: 2.66→34.965 Å / SU ML: 0.31 / 交差検証法: THROUGHOUT / σ(F): 2.01 / 位相誤差: 25.53 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2373 2258 7.1 %
Rwork0.2059 --
obs0.2081 31802 91.11 %
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
精密化ステップサイクル: LAST / 解像度: 2.66→34.965 Å
タンパク質核酸リガンド溶媒全体
原子数7510 0 56 153 7719
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0047662
X-RAY DIFFRACTIONf_angle_d0.72810324
X-RAY DIFFRACTIONf_dihedral_angle_d13.5262756
X-RAY DIFFRACTIONf_chiral_restr0.0261202
X-RAY DIFFRACTIONf_plane_restr0.0021302
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.71780.27611340.26261752X-RAY DIFFRACTION88
2.7178-2.7810.35981400.25261797X-RAY DIFFRACTION88
2.781-2.85050.3121470.26021828X-RAY DIFFRACTION91
2.8505-2.92760.26781340.25931836X-RAY DIFFRACTION90
2.9276-3.01370.27511540.23391842X-RAY DIFFRACTION90
3.0137-3.11090.27431440.24161817X-RAY DIFFRACTION91
3.1109-3.2220.25521270.2381869X-RAY DIFFRACTION91
3.222-3.35090.25911520.22541843X-RAY DIFFRACTION92
3.3509-3.50330.29731370.22381875X-RAY DIFFRACTION92
3.5033-3.68780.21151470.2111880X-RAY DIFFRACTION93
3.6878-3.91860.25171480.19881910X-RAY DIFFRACTION93
3.9186-4.22060.23231280.18421840X-RAY DIFFRACTION91
4.2206-4.64450.16281420.1551874X-RAY DIFFRACTION92
4.6445-5.31460.19661330.17481901X-RAY DIFFRACTION93
5.3146-6.68810.25231400.21451871X-RAY DIFFRACTION92
6.6881-34.96790.19831510.18221809X-RAY DIFFRACTION90
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)
10.10640.08590.05230.079-0.08350.08880.01390.19230.26630.08270.1664-0.01480.00290.127300.3694-0.0290.06190.3763-0.01780.237520.0859-12.467726.8233
2-0.00140.0060.00860.1189-0.02530.0570.2171-0.04170.1134-0.18560.0511-0.2703-0.0189-0.389200.33180.0221-0.16720.41810.00840.39641.0519-27.956125.3805
30.00890.0160.02590.00710.00980.04610.05470.097-0.0287-0.20030.05970.0586-0.1767-0.2469-0-0.79480.0206-1.06980.7660.1617-0.66080.0666-21.037217.5587
40.0990.16730.06530.1116-0.07560.1041-0.14170.0997-0.0856-0.06650.07570.05050.1001-0.111900.3179-0.0636-0.01410.3325-0.04070.26554.5416-29.475829.7281
50.03650.05670.113-0.00950.08440.1932-0.0329-0.10850.2310.25840.05870.0649-0.0373-0.099700.2222-0.0004-0.01560.24140.04330.32327.6626-21.772429.6128
60.0002-0.0196-0.02970.0045-0.0189-0.0032-0.17020.1335-0.0873-0.1156-0.03050.0827-0.14780.1228-00.89510.1304-0.34260.5292-0.02940.18698.71919.783516.0261
7-0.01760.0071-0.02180.0110.02360.0136-0.09960.0833-0.3883-0.2131-0.2641-0.0189-0.1382-0.0786-00.83280.0679-0.36110.4633-0.13330.64815.24355.631119.2699
8-0.0052-0.0215-0.0013-0.0078-0.00220.0034-0.13880.0748-0.0258-0.03940.0078-0.025-0.0532-0.0577-01.69550.38-0.14190.88820.22670.16851.869924.4586.2791
9-0.0086-0.00090.0097-0.0001-0.00180.00310.20310.12550.14-0.0675-0.13530.1224-0.0323-0.1545-00.82470.5296-1.18470.24370.2962-0.7737-0.692217.349315.3723
100.00220.00030.0010.00780.0069-0.0107-0.0048-0.0201-0.05680.0702-0.18830.1169-0.05250.0121-00.3754-0.3882-1.1994-0.0676-0.75720.7072-5.87566.486120.3875
11-0.0013-0.0031-0.006-0.0018-0.00130.002-0.2939-0.11920.03480.0109-0.11040.0765-0.02320.149400.54390.0949-0.18210.4982-0.08611.0822-8.60627.658227.6223
120.00190.015-0.0029-0.0154-0.0067-0.00130.2620.32820.2448-0.2937-0.0108-0.1556-0.28640.175700.70690.4029-0.64750.2760.14010.2172.273620.879617.9193
130.0179-0.00110.0540.02470.03410.03240.05580.09370.059-0.0818-0.33640.3806-0.2248-0.073500.4492-0.2225-0.368-0.2223-0.24880.5448-1.719417.728528.1055
140.0072-0.00860.0230.00430.0197-0.01350.1255-0.08450.0139-0.0577-0.1370.0797-0.2165-0.082800.40620.0513-0.10450.3976-0.03140.4383-0.957920.861832.4185
150.0198-0.0228-0.0219-0.00180.0053-0.00690.2060.133-0.3172-0.0921-0.02580.0095-0.29140.061-00.5825-0.0098-0.20030.5398-0.03590.47766.61317.280127.2937
16-0.00250.0032-0.0010.00640.00230.00040.04670.01550.0055-0.03290.04320.0093-0.02320.043100.86810.069-0.21620.5942-0.04511.1195-1.86124.872336.6499
17-0.00310.0022-0.01380.0043-0.0066-0.00490.0878-0.0038-0.0068-0.0354-0.0588-0.019-0.0238-0.1126-00.96140.438-0.22520.2781-0.20610.56718.445110.337225.1
180.00020.001-0.00060.0112-0.00640.0033-0.02370.07530.0240.0196-0.04230.00310.00290.02570.00011.49120.3056-0.15630.9945-0.11460.769814.524619.304511.2042
190.12480.007-0.07550.0677-0.17080.2515-0.0685-0.0431-0.06280.1380.02580.01650.06120.087600.21810.0247-0.05480.3253-0.01690.2272-9.45355.6242-5.3048
200.00260.00540.01070.0003-0.0104-0.00270.1684-0.01640.0024-0.0340.1870.07210.0865-0.366500.23290.0006-0.05050.40280.00580.47-36.365216.6705-6.125
210.03150.0376-0.0531-0.0085-0.03350.0067-0.2624-0.2236-0.10770.2367-0.05920.28340.1558-0.7256-00.0994-0.03850.35990.7450.0782-0.0138-28.31659.87032.5117
220.0096-0.00370.0103-0.0082-0.03650.0111-0.0809-0.11620.25020.3130.1655-0.0551-0.34050.1968-00.2905-0.0206-0.00350.29740.02260.3456-16.643220.837-1.991
230.0436-0.0078-0.02640.0019-0.03690.0692-0.0209-0.15810.1411-0.03110.04460.1775-0.0234-0.1692-00.18440.01840.0190.2626-0.0040.2578-27.937118.2338-14.0154
240.0165-0.0031-0.007600.00790.01920.0258-0.0247-0.1025-0.23590.4079-0.0202-0.13340.0729-00.24920.03260.0710.24540.00190.2865-19.892621.532-15.2191
250.0139-0.0139-0.00810.03680.01330.020.22630.2059-0.18220.0226-0.18880.01710.2254-0.034300.1325-0.05820.01650.21420.05010.3324-19.95265.9608-5.2923
260.06790.03340.01260.01870.00950.0104-0.0337-0.24810.51780.4258-0.04840.1830.0139-0.254-00.5824-0.02070.1440.4589-0.07860.4119-20.2214-20.48636.1412
270.1030.06660.06460.03780.09850.0278-0.0122-0.28850.02970.2208-0.32080.65450.0571-0.712200.3823-0.00710.20580.3737-0.04720.6219-31.0042-23.33391.1628
280.0422-0.0183-0.06160.06480.00920.05090.3129-0.14950.3642-0.06-0.26940.24520.26210.029300.3165-0.02590.13280.3333-0.03810.428-25.0726-29.3828-6.7534
290.1049-0.0246-0.1460.07420.110.0846-0.158-0.12610.10410.05120.04710.12390.1338-0.140500.39570.03850.02860.44550.00130.4878-19.024-22.8914-1.6786
300.020.04390.04530.05690.08640.0494-0.1725-0.23930.1227-0.17080.14220.0763-0.0391-0.0507-00.37750.00130.01260.2897-0.01660.5794-9.4235-15.1084-4.1034
310.00530.0068-0.00710.018-0.00740.0072-0.1599-0.3043-0.2210.29860.1377-0.15570.00580.050300.49070.04260.10960.33720.12480.508-4.3962-31.2119-12.6234
32-0.0094-0.00070.0017-0.0086-0.01690.00030.00950.2149-0.0282-0.1490.03320.0025-0.1487-0.0341-00.5147-0.05370.08410.54450.0340.4316-6.0486-30.758-31.7905
330.0260.0010.00740.0376-0.02930.0138-0.2330.10070.4467-0.22010.1497-0.2702-0.1243-0.086300.2803-0.1880.47140.3760.06690.69461.2962-24.465-23.0734
340.0166-0.01770.0190.01040.01880.0048-0.171-0.1874-0.04690.2732-0.2357-0.15360.56520.1543-00.54920.02890.16040.31310.00840.5276-3.6865-34.2048-12.2826
350.0185-0.01120.02360.0156-0.0120.02710.15860.17150.1207-0.42620.03390.06170.08090.020400.45290.01820.080.33750.07010.416-15.0722-31.8044-25.0062
360.0211-0.04410.11070.05370.00940.0155-0.02290.05750.2006-0.0893-0.0020.31460.07350.030600.3544-0.02640.11390.19060.06210.4008-11.3722-25.652-16.9927
370.00650.0037-0.00190.00260.0054-0.00110.0149-0.0012-0.0103-0.0713-0.0059-0.0724-0.02860.023100.5694-0.0278-0.07970.54570.07181.10613.4746-13.8584-14.65
380.0244-0.0458-0.03410.081-0.00150.102-0.1028-0.1292-0.275-0.3852-0.025-0.14640.09830.137-00.27820.0401-0.0040.3313-0.04330.3111.14714.4008-16.1555
390.00950.0514-0.0327-0.01710.0222-0.04740.0720.30140.24-0.1429-0.1574-0.1728-0.37130.3678-0-2.1963-0.76451.83430.18930.3873-0.94179.444317.9966-20.8717
400.0146-0.04470.02580.01750.02590.01870.08280.2119-0.03480.0105-0.0434-0.12510.0318-0.0074-00.20560.0050.01590.3677-0.02230.2378-4.0763.7529-30.9373
410.0931-0.0729-0.09880.09460.00970.0287-0.13160.07130.4875-0.28450.0755-0.0133-0.4937-0.0512-00.17830.05410.00460.20890.00660.2217-6.860216.9718-23.7243
42-0.0096-0.01510.0147-0.00980.01660.0176-0.2241-0.0960.08210.31130.16610.0296-0.0183-0.2825-00.1958-0.0092-0.00360.3043-0.03190.2626-9.283511.541-16.326
430.03960.0173-0.0658-0.0109-0.00170.0324-0.1298-0.00340.1408-0.04720.01330.13590.0486-0.2111-00.1583-0.03490.01620.2970.02180.3815-10.57855.2113-20.1445
44-0.0016-0.00270.02040.0033-0.00970.00470.1593-0.17440.0460.20870.2699-0.0162-0.276-0.1163-00.477-0.04210.13190.8414-0.22560.178.230919.6473-7.729
450.0508-0.0901-0.05820.07750.06710.0744-0.21430.4223-0.01390.09940.15940.4213-0.01440.236300.668-0.0076-0.00660.2463-0.02850.473917.58334.979224.6732
460.0013-0.01960.01050.00890.00040.0001-0.15120.13270.1758-0.2430.1220.00650.03870.0032-00.5742-0.04680.01390.28940.10640.419222.648920.988934.1816
470.01030.0211-0.01340.02660.00720.0108-0.1524-0.247-0.38910.0760.1399-0.32850.075-0.1206-00.50240.0795-0.14880.35810.03850.550826.717615.663145.9982
48-0.0002-0.0024-0.01030.00030.01980.01-0.23830.17570.1773-0.3397-0.049-0.1977-0.1558-0.2633-00.5864-0.0927-0.12270.40160.01320.475823.293923.776833.2315
490.01370.00920.04930.00340.01650.00990.4845-0.0394-0.11650.75760.0153-0.2050.2215-0.361800.56910.0013-0.32850.34760.08530.442712.005721.200645.7996
500.0044-0.00190.01920.00450.00650.01320.11150.01560.13230.1446-0.06680.1632-0.01180.1512-00.4481-0.0115-0.13920.3556-0.01550.33789.981724.747638.1979
51-0.0003-0.003-0.00670.01260.02490.0477-0.12350.0856-0.1342-0.03610.05230.12380.2214-0.1053-00.68540.0498-0.09010.26270.05440.449520.90818.481837.292
520.00270.0115-0.00620.039-0.01640.0245-0.01530.14750.22750.1882-0.06830.0417-0.08120.015900.2709-0.09520.02590.405-0.05220.211830.4238-16.835734.5359
530.01610.01910.02820.03830.02230.0433-0.10140.18550.00180.05790.0373-0.1229-0.27080.2021-00.2808-0.0648-0.01870.36180.00590.401726.8132-12.826438.6842
540.008-0.0058-0.0036-0.0036-0.02090.0008-0.0145-0.1788-0.0490.18530.0898-0.16320.01860.105500.43320.155-0.06740.56570.01480.602441.2741-30.670539.7912
550.01450.00890.064-0.02430.1790.054-0.0404-0.28540.11610.0580.10470.01970.03080.0674-00.2316-0.0181-0.00810.3433-0.02080.164325.8045-17.030749.4784
560.08320.10090.06950.11340.040.06910.1228-0.1116-0.34430.1553-0.044-0.0580.3453-0.077500.2308-0.0142-0.01630.27680.00280.175920.8607-26.048344.1585
570.12790.07290.12150.0962-0.02410.12470.0424-0.0529-0.09010.2324-0.13530.18680.0251-0.036100.2802-0.0381-0.02610.35470.04460.166417.8581-21.10141.2094
58-0.0021-0.0049-0.00870.00390.00280.00650.11870.0878-0.0988-0.05580.00270.0180.1311-0.0127-00.4160.01150.01930.8921-0.26210.51935.3893-29.972329.0043
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 103 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 189 )
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 216 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 246 )
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 259 )
8X-RAY DIFFRACTION8chain 'A' and (resid 260 through 269 )
9X-RAY DIFFRACTION9chain 'A' and (resid 270 through 276 )
10X-RAY DIFFRACTION10chain 'A' and (resid 277 through 286 )
11X-RAY DIFFRACTION11chain 'A' and (resid 287 through 296 )
12X-RAY DIFFRACTION12chain 'A' and (resid 297 through 305 )
13X-RAY DIFFRACTION13chain 'A' and (resid 306 through 319 )
14X-RAY DIFFRACTION14chain 'A' and (resid 320 through 328 )
15X-RAY DIFFRACTION15chain 'A' and (resid 329 through 340 )
16X-RAY DIFFRACTION16chain 'A' and (resid 341 through 348 )
17X-RAY DIFFRACTION17chain 'A' and (resid 349 through 355 )
18X-RAY DIFFRACTION18chain 'A' and (resid 356 through 363 )
19X-RAY DIFFRACTION19chain 'B' and (resid 103 through 128 )
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 137 )
21X-RAY DIFFRACTION21chain 'B' and (resid 138 through 157 )
22X-RAY DIFFRACTION22chain 'B' and (resid 158 through 171 )
23X-RAY DIFFRACTION23chain 'B' and (resid 172 through 189 )
24X-RAY DIFFRACTION24chain 'B' and (resid 190 through 199 )
25X-RAY DIFFRACTION25chain 'B' and (resid 200 through 216 )
26X-RAY DIFFRACTION26chain 'B' and (resid 236 through 265 )
27X-RAY DIFFRACTION27chain 'B' and (resid 266 through 301 )
28X-RAY DIFFRACTION28chain 'B' and (resid 302 through 340 )
29X-RAY DIFFRACTION29chain 'B' and (resid 341 through 365 )
30X-RAY DIFFRACTION30chain 'C' and (resid 103 through 122 )
31X-RAY DIFFRACTION31chain 'C' and (resid 123 through 128 )
32X-RAY DIFFRACTION32chain 'C' and (resid 129 through 137 )
33X-RAY DIFFRACTION33chain 'C' and (resid 138 through 157 )
34X-RAY DIFFRACTION34chain 'C' and (resid 158 through 171 )
35X-RAY DIFFRACTION35chain 'C' and (resid 172 through 189 )
36X-RAY DIFFRACTION36chain 'C' and (resid 190 through 214 )
37X-RAY DIFFRACTION37chain 'C' and (resid 215 through 219 )
38X-RAY DIFFRACTION38chain 'C' and (resid 237 through 259 )
39X-RAY DIFFRACTION39chain 'C' and (resid 260 through 276 )
40X-RAY DIFFRACTION40chain 'C' and (resid 277 through 296 )
41X-RAY DIFFRACTION41chain 'C' and (resid 297 through 331 )
42X-RAY DIFFRACTION42chain 'C' and (resid 332 through 340 )
43X-RAY DIFFRACTION43chain 'C' and (resid 341 through 356 )
44X-RAY DIFFRACTION44chain 'C' and (resid 357 through 367 )
45X-RAY DIFFRACTION45chain 'D' and (resid 103 through 122 )
46X-RAY DIFFRACTION46chain 'D' and (resid 123 through 128 )
47X-RAY DIFFRACTION47chain 'D' and (resid 129 through 157 )
48X-RAY DIFFRACTION48chain 'D' and (resid 158 through 171 )
49X-RAY DIFFRACTION49chain 'D' and (resid 172 through 189 )
50X-RAY DIFFRACTION50chain 'D' and (resid 190 through 199 )
51X-RAY DIFFRACTION51chain 'D' and (resid 200 through 218 )
52X-RAY DIFFRACTION52chain 'D' and (resid 237 through 246 )
53X-RAY DIFFRACTION53chain 'D' and (resid 247 through 259 )
54X-RAY DIFFRACTION54chain 'D' and (resid 260 through 269 )
55X-RAY DIFFRACTION55chain 'D' and (resid 270 through 296 )
56X-RAY DIFFRACTION56chain 'D' and (resid 297 through 324 )
57X-RAY DIFFRACTION57chain 'D' and (resid 325 through 356 )
58X-RAY DIFFRACTION58chain 'D' and (resid 357 through 367 )

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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