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- PDB-8byw: Rut B structure -

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基本情報

登録情報
データベース: PDB / ID: 8byw
タイトルRut B structure
要素Ureidoacrylate amidohydrolase RutB
キーワードHYDROLASE
機能・相同性
機能・相同性情報


ureidoacrylate amidohydrolase / uracil catabolic process / nitrogen utilization / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
類似検索 - 分子機能
Ureidoacrylate amidohydrolase RutB / : / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Ureidoacrylate amidohydrolase RutB
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.59 Å
データ登録者Rajendran, C. / Sterner, R. / Busch, M.
資金援助 ドイツ, 1件
組織認可番号
German Research Foundation (DFG) ドイツ
引用ジャーナル: Biochemistry / : 2023
タイトル: Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli .
著者: Busch, M.R. / Rajendran, C. / Sterner, R.
履歴
登録2022年12月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年1月25日Provider: repository / タイプ: Initial release
改定 1.12023年2月15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.title / _citation_author.identifier_ORCID
改定 1.22023年11月15日Group: Data collection / Source and taxonomy
カテゴリ: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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: Ureidoacrylate amidohydrolase RutB
B: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB
D: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB
F: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB
I: Ureidoacrylate amidohydrolase RutB
J: Ureidoacrylate amidohydrolase RutB
K: Ureidoacrylate amidohydrolase RutB
L: Ureidoacrylate amidohydrolase RutB
M: Ureidoacrylate amidohydrolase RutB
N: Ureidoacrylate amidohydrolase RutB
O: Ureidoacrylate amidohydrolase RutB
P: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)403,67316
ポリマ-403,67316
非ポリマー00
55,9193104
1
A: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-19 kcal/mol
Surface area16150 Å2
手法PISA
2
B: Ureidoacrylate amidohydrolase RutB
I: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-21 kcal/mol
Surface area16080 Å2
手法PISA
3
D: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-21 kcal/mol
Surface area16110 Å2
手法PISA
4
E: Ureidoacrylate amidohydrolase RutB

N: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation1_546x,y-1,z+11
Buried area3700 Å2
ΔGint-22 kcal/mol
Surface area16050 Å2
手法PISA
5
F: Ureidoacrylate amidohydrolase RutB

H: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3670 Å2
ΔGint-18 kcal/mol
Surface area16150 Å2
手法PISA
6
J: Ureidoacrylate amidohydrolase RutB

L: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area3680 Å2
ΔGint-20 kcal/mol
Surface area15950 Å2
手法PISA
7
K: Ureidoacrylate amidohydrolase RutB

M: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3670 Å2
ΔGint-21 kcal/mol
Surface area16220 Å2
手法PISA
8
O: Ureidoacrylate amidohydrolase RutB

P: Ureidoacrylate amidohydrolase RutB


分子量 (理論値)分子数
合計 (水以外)50,4592
ポリマ-50,4592
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3670 Å2
ΔGint-21 kcal/mol
Surface area16220 Å2
手法PISA
単位格子
Length a, b, c (Å)69.562, 108.252, 123.744
Angle α, β, γ (deg.)85.74, 83.33, 74.27
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Ureidoacrylate amidohydrolase RutB


分子量: 25229.562 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
遺伝子: rutB, EcDH1_2631, ECDH1ME8569_0965 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: C9QZ65, ureidoacrylate amidohydrolase
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3104 / 由来タイプ: 天然 / : 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: 2.2 Å3/Da / 溶媒含有率: 44.21 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 300K / 検出器: PIXEL / 日付: 2019年3月15日
放射プロトコル: 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 Å / 相対比: 1
反射解像度: 1.59→48.71 Å / Num. obs: 447821 / % possible obs: 96.55 % / 冗長度: 3.5 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 7.55
反射 シェル解像度: 1.59→1.647 Å / Num. unique obs: 43730 / CC1/2: 0.481

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18rc2精密化
XDSデータ削減
XSCALE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 / 解像度: 1.59→48.71 Å / SU ML: 0.23 / 交差検証法: FREE R-VALUE / σ(F): 0.9 / 位相誤差: 25.41 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2329 43234 5 %
Rwork0.2062 --
obs0.2075 447821 92.48 %
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: 1.59→48.71 Å
タンパク質核酸リガンド溶媒全体
原子数27429 0 0 3104 30533
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00628037
X-RAY DIFFRACTIONf_angle_d0.85238242
X-RAY DIFFRACTIONf_dihedral_angle_d5.9553744
X-RAY DIFFRACTIONf_chiral_restr0.0524256
X-RAY DIFFRACTIONf_plane_restr0.0065005
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.60.370710470.349620288X-RAY DIFFRACTION69
1.6-1.620.343314620.338227703X-RAY DIFFRACTION93
1.62-1.640.358714430.328627317X-RAY DIFFRACTION92
1.64-1.660.330314250.315827452X-RAY DIFFRACTION93
1.66-1.680.317214600.302427552X-RAY DIFFRACTION93
1.68-1.710.322414400.299227448X-RAY DIFFRACTION93
1.71-1.730.312414550.292427518X-RAY DIFFRACTION93
1.73-1.760.323314400.285727384X-RAY DIFFRACTION93
1.76-1.790.306414640.275927603X-RAY DIFFRACTION93
1.79-1.810.290414400.259227424X-RAY DIFFRACTION93
1.81-1.850.271514570.260427555X-RAY DIFFRACTION93
1.85-1.880.285514490.252327488X-RAY DIFFRACTION93
1.88-1.920.28814520.259927577X-RAY DIFFRACTION93
1.92-1.950.284414490.254127326X-RAY DIFFRACTION93
1.95-20.255114510.227327689X-RAY DIFFRACTION93
2-2.040.250114560.214127687X-RAY DIFFRACTION93
2.04-2.090.245714470.205827699X-RAY DIFFRACTION94
2.09-2.150.235814610.199927780X-RAY DIFFRACTION94
2.15-2.210.24314550.202927675X-RAY DIFFRACTION93
2.21-2.290.239714440.209827536X-RAY DIFFRACTION93
2.29-2.370.23414530.193327682X-RAY DIFFRACTION93
2.37-2.460.220714600.184227786X-RAY DIFFRACTION94
2.46-2.570.221914700.190827935X-RAY DIFFRACTION94
2.57-2.710.231414600.191827758X-RAY DIFFRACTION94
2.71-2.880.21514820.194628084X-RAY DIFFRACTION95
2.88-3.10.221714640.186127950X-RAY DIFFRACTION94
3.1-3.410.212914520.184627827X-RAY DIFFRACTION94
3.41-3.910.191414500.171227289X-RAY DIFFRACTION92
3.91-4.920.175414770.158127981X-RAY DIFFRACTION94
4.92-48.710.196114690.188928089X-RAY DIFFRACTION95
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2942-0.08730.59530.9883-0.32251.2878-0.0163-0.0161-0.1314-0.07820.0228-0.05890.12430.016-0.0050.14010.01220.03970.1444-0.01940.148829.5441-14.041216.4848
20.9976-0.5760.00531.17180.23880.47150.03080.09540.0031-0.1519-0.0165-0.03680.03710.01650.01890.1748-0.00310.00630.16330.00180.145723.7806-9.055811.2419
30.6735-0.38470.20121.4304-0.00111.0499-0.0270.05470.0032-0.0605-0.0260.08540.0232-0.04330.04350.1407-0.0237-0.00360.16670.00240.118719.5062-1.46538.3131
40.95380.23840.17390.87740.1420.1785-0.00720.0074-0.060.0013-0.01760.02360.075-0.01460.0280.1614-0.00290.00950.1398-0.01220.144420.5656-12.885622.3583
50.4328-0.2120.05810.7545-0.13320.4788-0.05030.0004-0.0018-0.02670.0068-0.12670.01080.07820.05710.1084-0.00640.00480.1362-0.01290.154132.441-8.832623.8774
61.5947-0.2143-0.24362.83491.18553.17760.00080.1463-0.2846-0.07750.013-0.18460.43120.26270.04820.18770.0343-0.00140.1508-0.01460.216836.0974-22.224719.739
71.1108-0.82550.84860.9852-0.61170.73170.03780.1592-0.0217-0.1285-0.0908-0.18870.02780.10160.01070.16410.00880.01380.18480.01030.191951.5689-63.344219.7575
81.2201-0.44770.15271.1048-0.05460.28160.08620.23410.0044-0.1535-0.0943-0.03540.01640.0294-0.02280.17860.00930.00730.2150.02650.137345.2594-59.035814.5531
90.1908-0.13240.15370.1544-0.22432.37690.02240.06350.11670.0994-0.0567-0.0036-0.3450.42180.04890.2276-0.019-0.03160.20370.02680.185939.3023-41.279917.7388
100.4553-0.57370.17491.872-0.57320.80050.0180.1036-0.0424-0.1976-0.02070.08560.1330.0120.00080.1947-0.00170.00760.20450.00620.134140.4383-56.87468.9754
110.6891-0.17750.16211.07950.16480.1144-0.00340.0205-0.08520.0391-0.0226-0.02920.04010.01350.06120.1475-0.00350.01380.17350.01030.160442.5554-63.348125.616
120.7156-0.41390.20330.79750.08430.7394-0.0347-0.01660.08810.0186-0.0535-0.1437-0.03380.18130.10180.1205-0.0174-0.00640.16620.03750.179253.8179-57.820827.1211
132.0991-0.6016-0.61143.1221.75863.9298-0.05150.1198-0.18970.07920.0964-0.29720.46790.4043-0.0420.1510.00850.00290.17490.00110.255959.1196-70.585222.945
140.60710.06250.26921.8052-0.85581.44220.0308-0.05910.03160.237-0.0327-0.1513-0.09270.13010.01340.1542-0.003-0.04480.1509-0.02780.180928.64498.385237.4999
150.6460.0593-0.20081.79260.01120.8998-0.0073-0.10070.04170.2939-0.024-0.1893-0.04280.07060.03310.1585-0.0168-0.05060.1758-0.00510.168729.87132.017944.1178
160.67030.81481.17871.45390.79753.2718-0.12940.0353-0.17270.26310.1015-0.23790.16830.3569-0.00460.20930.0389-0.03590.21320.01520.178335.6077-15.748640.6074
170.440.3247-0.11841.9746-0.20911.19740.1296-0.2991-0.19030.5076-0.2315-0.2820.07030.19320.11090.3171-0.0259-0.14080.29060.02330.245935.3208-7.512251.4717
180.8449-0.13320.04151.68770.50450.99430.034-0.33130.16970.6915-0.1310.0540.0797-0.05140.08860.2528-0.0208-0.02290.2201-0.05290.182124.57586.447349.6921
190.91660.0199-0.24021.2170.06930.6039-0.00380.03310.01210.0647-0.05020.0364-0.0641-0.04620.03790.1331-0.0164-0.00870.1319-0.00840.130620.20761.766436.7188
200.2522-0.22150.32060.60130.1330.4577-0.06750.04060.0650.00330.0531-0.1165-0.0620.08840.05310.1208-0.0222-0.00070.1516-0.00330.165629.8394.327829.0181
211.2963-0.79-0.38412.0831.26242.2967-0.1545-0.02720.2908-0.11530.0611-0.0336-0.35430.11490.10050.2579-0.0023-0.03990.1293-0.01080.231227.264118.111232.558
221.0306-0.00720.24261.1960.41311.0866-0.0279-0.0816-0.16680.04210.0755-0.03760.09850.0992-0.03360.1898-0.00010.00260.11740.04010.142226.1495-75.241150.2669
230.6803-0.12360.17781.4646-0.23390.8652-0.048-0.1474-0.03620.18920.05140.04680.05440.02520.01270.17150.0251-0.0010.15990.00610.11827.1007-67.68355.52
240.5918-0.2590.05791.0399-0.22760.787-0.0524-0.14240.04180.10990.0214-0.0324-0.00250.03490.05030.18110.0177-0.01690.1787-0.0120.119225.2194-59.161258.3889
251.1023-0.31420.14360.7670.01570.21-0.00610.0436-0.04040.0071-0.0177-0.10530.06890.02750.05620.16270.0027-0.00230.12910.01610.133631.9539-68.313944.3963
260.85110.2132-0.08470.85260.04521.316-0.0403-0.0646-0.15430.01570.01860.04170.2385-0.05160.00550.1588-0.0174-0.00230.11670.01490.169822.185-76.712444.0217
270.898-0.2864-0.31970.92090.21481.1256-0.0231-0.01950.121-0.00640.02960.0663-0.08080.01120.02840.16180.0282-0.02540.15350.00880.155833.1217-82.267481.4582
280.8508-0.4403-0.11071.22930.04140.5241-0.02570.06910.0065-0.07260.00640.0517-0.0359-0.03880.03090.17460.0201-0.00850.16050.00220.118837.5716-87.719575.472
290.6774-0.37730.31440.24580.17022.67090.0483-0.1109-0.21030.0182-0.0130.03510.2449-0.30960.07650.26060.01120.0140.19460.00550.166342.0482-105.824379.1196
300.548-0.21210.18491.71960.25440.7963-0.04360.1094-0.0046-0.2320.047-0.0708-0.0610.0783-0.01650.1935-0.0029-0.00220.16330.00440.127540.7751-90.945769.28
310.85580.4275-0.14260.9092-0.20690.23120.0035-0.02320.02690.0539-0.0581-0.075-0.0507-0.0060.05830.16940.024-0.01710.16080.0050.128943.1815-83.040385.1809
320.8987-0.36320.15090.72990.0230.8949-0.0865-0.0818-0.01420.06150.00240.13230.038-0.08660.05930.15540.02740.02760.16350.01010.159532.039-86.795289.7478
331.899-0.56250.4322.3179-0.72842.3297-0.1679-0.03140.25110.07750.11080.1456-0.5866-0.33890.040.20010.0535-0.00990.1487-0.01440.204727.4075-73.751985.3937
341.027-0.5504-0.47510.80640.66911.70140.05540.1661-0.0514-0.1258-0.09690.163-0.1072-0.27260.01150.13160.015-0.05470.2203-0.02920.254660.3609-3.549325.5148
351.359-0.48760.08070.87090.15011.0763-0.0020.1664-0.0514-0.1355-0.11180.22440.0102-0.28490.05090.1444-0.0131-0.02950.2268-0.05590.203363.0579-9.671819.0658
360.5178-0.12480.64280.25230.322.0217-0.19130.1149-0.3801-0.17260.120.01760.1954-0.2838-0.00950.1849-0.07550.01730.1984-0.05730.261468.1965-27.395922.9717
371.44380.0288-0.07531.32860.25560.9274-0.06090.3619-0.1028-0.4403-0.07920.20810.0121-0.2190.07890.2133-0.0141-0.0650.3128-0.0720.217264.3968-13.4612.5016
380.46230.2538-0.32220.9993-0.13760.4277-0.0174-0.01410.06910.0177-0.02720.0688-0.088-0.0620.02780.1204-0.007-0.00970.1649-0.02090.172271.0391-4.250226.4909
390.45490.1272-0.08290.92880.13760.7546-0.01550.0096-0.0251-0.0367-0.06950.2909-0.0406-0.28320.05030.107-0.01360.01150.1873-0.03520.217761.5712-7.426834.1483
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611.46390.2140.2413.01941.66553.2082-0.2461-0.13860.4442-0.1012-0.21690.2694-0.8754-0.09860.11350.3213-0.0143-0.12480.14570.00460.329845.3278-31.93236.3982
620.5738-0.1105-0.06560.9879-0.65260.98770.0576-0.07470.07650.0752-0.0678-0.0805-0.06410.0928-0.04920.185-0.0168-0.03980.1738-0.01230.176851.7381-77.0774-18.6459
630.7424-0.0136-0.10871.3649-0.43060.3976-0.0187-0.13220.06110.1828-0.0084-0.1277-0.07790.10.01250.21650.0009-0.04680.2484-0.00150.16651.3413-84.0013-12.5309
640.3838-0.18250.52280.8221-0.69610.7249-0.0365-0.11490.02840.0277-0.00370.0081-0.06890.06650.02480.20820.0159-0.02790.2350.00340.143252.9731-92.3836-9.1971
651.0974-0.3303-0.26151.2890.08720.26450.0048-0.01330.0520.0571-0.05620.0721-0.0350.05580.05250.17070.0113-0.02910.17080.00270.143943.9999-83.568-22.2569
660.38040.04070.0190.7776-0.06730.9741-0.01080.02640.0045-0.0087-0.051-0.1629-0.03070.21480.03990.1605-0.0023-0.0130.21780.02790.196955.2899-80.3573-26.8011
671.7811-0.3348-0.25373.27991.87983.8064-0.0333-0.11620.42110.1530.003-0.1233-0.65780.10020.03770.2886-0.0002-0.01790.1701-0.00870.267951.5373-66.9762-22.7707
680.7565-0.213-0.13490.9523-0.33640.96920.04830.0510.1343-0.0757-0.0480.0503-0.1294-0.0529-0.00440.24530.0286-0.03190.1402-0.02870.181329.0809-23.9217-14.6405
690.4272-0.1992-0.03071.1641-0.13840.6293-0.0247-0.09660.03430.03470.0089-0.0351-0.02440.00370.00460.21290.0231-0.01290.1569-0.02130.145929.4637-30.9955-8.7068
700.8796-0.39250.08721.2609-0.02010.71180.0105-0.0983-0.0088-0.0414-0.0319-0.01-0.0302-0.01310.02350.18670.0177-0.00430.16830.00010.106832.0938-39.2181-5.6221
711.4047-0.0336-0.31561.01620.15850.1346-0.0407-0.05130.0667-0.0722-0.03740.1278-0.133-0.06080.0980.21980.0269-0.02510.1382-0.02370.124422.142-31.2511-18.409
720.89020.04790.33941.1601-0.37341.0792-0.03380.0320.1542-0.1145-0.0477-0.1041-0.15410.01960.03640.23670.02320.0030.1348-0.00160.175931.4564-23.0074-21.7576
731.2048-0.74180.67170.7527-0.48311.55310.1290.23960.0433-0.1956-0.1626-0.08580.25380.3484-0.01850.2430.08080.0580.30490.04670.20243.5345-92.114582.3774
740.979-0.4978-0.19010.8844-0.03561.0094-0.01150.11730.0734-0.2284-0.0659-0.18070.16950.25780.01660.24680.07050.02750.29130.04720.1939-0.5632-86.610376.1951
750.5897-0.235-0.43420.1789-0.0352.1606-0.0085-0.00390.6029-0.19270.0565-0.0331-0.22570.3441-0.05770.226-0.0313-0.02250.24780.0890.266-5.044-68.560379.5311
761.4592-0.0192-0.0381.4472-0.03870.9343-0.04040.40080.0537-0.4948-0.0474-0.02520.08340.14390.0290.2510.04870.0550.35260.0760.1736-3.3978-83.415969.8148
770.9260.36030.16690.7506-0.01470.5502-0.0222-0.0269-0.0775-0.02240.0117-0.08270.21430.1710.01770.16970.0480.01470.19180.02110.143-6.6733-91.360585.6437
780.59280.1215-0.28880.6786-0.41690.69150.02450.1080.0101-0.0538-0.0617-0.2510.07760.32730.01640.14840.03620.00940.24630.03040.19024.2398-87.511590.6576
791.8506-0.5671-0.75482.23650.86032.18980.02720.0095-0.21990.1136-0.2995-0.34550.79490.52970.01590.39850.2710.06440.28480.12340.28029.1226-100.524586.6412
801.3865-0.67330.4971.0576-0.70351.42320.13380.33460.0346-0.2908-0.1135-0.1402-0.00970.1062-0.06150.29720.03430.05620.21370.00630.172752.8528-37.506285.9104
811.5526-0.98970.06561.01480.30790.74870.11390.28390.1227-0.3842-0.1198-0.1615-0.04780.17220.04530.35420.01910.05410.28380.0250.173747.9629-32.475679.7922
821.4281-0.37750.20660.47640.0670.88350.03560.32070.138-0.3964-0.1355-0.1491-0.12090.0010.06190.42060.05150.04340.27970.05580.151443.4353-24.913576.731
831.24310.18110.09221.27490.25070.64920.06710.1595-0.0605-0.1404-0.05070.05130.06850.0456-0.01440.26510.03330.00150.1918-0.01160.122942.5982-38.094389.2029
840.5533-0.1595-0.1130.95160.15111.0407-0.0167-0.00680.0428-0.193-0.0357-0.1836-0.06240.19350.05110.2310.01860.03260.18910.01080.176252.9469-32.938294.2536
850.918-0.16220.05872.35660.88341.322-0.04380.1579-0.1759-0.2592-0.0088-0.13180.30130.35270.08780.31630.07380.05320.2379-0.01920.22659.3581-45.122390.0054
860.63460.5019-0.15451.36590.72861.3031-0.0023-0.1806-0.08840.44460.06960.23590.11530.0003-0.10010.27570.04280.06050.23730.06120.183354.0351-4.1284-19.1783
870.83530.20050.20572.1842-0.20330.9904-0.0546-0.2694-0.04850.49550.04210.20790.0949-0.10530.02330.26420.02030.05430.29520.01860.150954.2782.8794-13.0455
880.45930.4804-0.39110.8958-0.76371.5493-0.119-0.11870.35120.15220.14570.3422-0.1113-0.2957-0.06160.27920.05890.02520.2952-0.04260.22847.582420.1106-16.5804
890.9941-0.06660.17012.60710.10170.89110.0692-0.47840.25560.4895-0.02810.3627-0.0852-0.15870.05880.41550.06150.12640.3543-0.0070.24950.528812.963-5.4878
900.8841-0.30540.27991.5431-0.34450.48110.0921-0.337-0.18770.3513-0.1414-0.08680.15590.3321-0.05230.32480.0441-0.00370.29090.06150.206561.2869-1.0041-8.6756
911.1376-0.27090.38960.9946-0.16330.48130.0228-0.0909-0.02720.1401-0.03-0.08410.07040.0932-0.00560.18740.02120.00960.17780.0130.114162.00832.3674-22.4494
920.57340.1182-0.24550.9946-0.1920.9977-0.0702-0.1161-0.0950.11080.03880.18150.1286-0.10580.04450.18030.01170.02670.17110.01330.161650.8829-0.7628-27.5658
931.4548-1.02110.55981.9586-0.88381.97520.0365-0.1101-0.3819-0.1522-0.04340.13560.51040.09910.00890.29050.02930.03580.21260.06550.239254.2938-14.0625-23.3877
940.5644-0.4225-0.39971.0860.71430.82910.01360.136-0.031-0.1603-0.0290.2904-0.0456-0.10.00570.25260.0457-0.05740.2111-0.03320.219111.9265-32.700785.364
951.2127-0.1436-0.2790.94810.2120.2471-0.00970.163-0.0104-0.1853-0.02280.11640.0229-0.11880.02360.29280.0312-0.06130.2446-0.05080.161516.9329-37.516779.2467
960.36460.11120.0860.81850.82360.5724-0.07310.03840.0291-0.08030.0310.0593-0.0691-0.04660.05090.29390.0341-0.04750.2278-0.0430.156921.3492-44.823675.9124
970.71930.1634-0.25161.3973-0.26790.23310.00760.07030.09290.0736-0.05850.0332-0.0126-0.040.03060.2560.0345-0.04720.1688-0.03930.16122.0003-32.31388.9573
980.5348-0.155-0.11620.6547-0.09351.1894-0.0451-0.0605-0.0681-0.0149-0.03550.19470.079-0.20410.10460.22690.0094-0.00150.1837-0.0450.242411.4975-37.557693.5071
992.0172-0.63271.1992.279-1.63033.2005-0.0961-0.00240.3379-0.0758-0.06650.3099-0.5258-0.32050.02470.31260.081-0.06150.2283-0.04060.32235.2713-25.129789.5272
1000.59310.32390.00831.45030.85431.2477-0.045-0.0755-0.01650.4080.03130.15650.3122-0.0453-0.02570.32840.00530.0710.22120.02410.21226.2161-58.18-15.6688
1010.5782-0.07570.04351.68750.09690.9109-0.1003-0.2201-0.03770.44750.02340.25020.2415-0.17970.05390.3502-0.01340.07910.2618-0.02040.20015.511-51.332-9.4596
1020.09550.04920.23760.8275-0.39731.925-0.0162-0.36010.23540.0663-0.00230.30820.1699-0.1233-0.10110.2530.01870.02250.2655-0.08190.2545-3.3158-34.9853-12.8115
1030.85860.16750.32061.52540.0061.1313-0.2572-0.48670.28390.91450.02190.2840.045-0.35690.060.406-0.02650.16810.3842-0.08940.25610.6155-41.8552-1.6956
1040.9035-0.1157-0.01331.4967-0.59991.09430.0623-0.255-0.18650.5796-0.14030.04980.53120.07270.01310.4442-0.02720.05660.2850.02280.208112.471-54.6138-4.9576
1052.2992-1.2619-0.12811.57210.57830.2931-0.10190.00860.03620.11080.0223-0.02910.148-0.01170.06440.23330.0210.0140.1736-0.01470.155116.055-47.0332-18.3681
1060.2095-0.39870.25011.1391-0.1050.5459-0.12410.2617-0.24810.1218-0.05810.06210.4279-0.01580.10110.34740.01850.02040.208-0.02820.2149.1775-56.0226-19.6642
1070.7369-0.22260.19390.9154-0.15290.86520.0167-0.0866-0.0890.1321-0.0280.17470.1387-0.1121-0.02760.2468-0.00960.01540.175-0.04420.18712.6144-55.2168-23.9697
1081.08070.03980.01351.7442-1.16652.363-0.09450.0252-0.3798-0.1731-0.1224-0.11980.94750.00890.02250.5110.03090.08860.1447-0.0050.30717.8389-68.1469-19.9391
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 38 )
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 100 )
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 133 )
11X-RAY DIFFRACTION11chain 'B' and (resid 134 through 165 )
12X-RAY DIFFRACTION12chain 'B' and (resid 166 through 207 )
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 223 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 38 )
15X-RAY DIFFRACTION15chain 'C' and (resid 39 through 86 )
16X-RAY DIFFRACTION16chain 'C' and (resid 87 through 100 )
17X-RAY DIFFRACTION17chain 'C' and (resid 101 through 119 )
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 133 )
19X-RAY DIFFRACTION19chain 'C' and (resid 134 through 165 )
20X-RAY DIFFRACTION20chain 'C' and (resid 166 through 207 )
21X-RAY DIFFRACTION21chain 'C' and (resid 208 through 223 )
22X-RAY DIFFRACTION22chain 'D' and (resid 3 through 38 )
23X-RAY DIFFRACTION23chain 'D' and (resid 39 through 86 )
24X-RAY DIFFRACTION24chain 'D' and (resid 87 through 133 )
25X-RAY DIFFRACTION25chain 'D' and (resid 134 through 165 )
26X-RAY DIFFRACTION26chain 'D' and (resid 166 through 223 )
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 38 )
28X-RAY DIFFRACTION28chain 'E' and (resid 39 through 86 )
29X-RAY DIFFRACTION29chain 'E' and (resid 87 through 100 )
30X-RAY DIFFRACTION30chain 'E' and (resid 101 through 133 )
31X-RAY DIFFRACTION31chain 'E' and (resid 134 through 165 )
32X-RAY DIFFRACTION32chain 'E' and (resid 166 through 207 )
33X-RAY DIFFRACTION33chain 'E' and (resid 208 through 223 )
34X-RAY DIFFRACTION34chain 'F' and (resid 3 through 38 )
35X-RAY DIFFRACTION35chain 'F' and (resid 39 through 86 )
36X-RAY DIFFRACTION36chain 'F' and (resid 87 through 100 )
37X-RAY DIFFRACTION37chain 'F' and (resid 101 through 133 )
38X-RAY DIFFRACTION38chain 'F' and (resid 134 through 165 )
39X-RAY DIFFRACTION39chain 'F' and (resid 166 through 207 )
40X-RAY DIFFRACTION40chain 'F' and (resid 208 through 223 )
41X-RAY DIFFRACTION41chain 'G' and (resid 3 through 38 )
42X-RAY DIFFRACTION42chain 'G' and (resid 39 through 86 )
43X-RAY DIFFRACTION43chain 'G' and (resid 87 through 133 )
44X-RAY DIFFRACTION44chain 'G' and (resid 134 through 165 )
45X-RAY DIFFRACTION45chain 'G' and (resid 166 through 207 )
46X-RAY DIFFRACTION46chain 'G' and (resid 208 through 223 )
47X-RAY DIFFRACTION47chain 'H' and (resid 3 through 38 )
48X-RAY DIFFRACTION48chain 'H' and (resid 39 through 86 )
49X-RAY DIFFRACTION49chain 'H' and (resid 87 through 100 )
50X-RAY DIFFRACTION50chain 'H' and (resid 101 through 133 )
51X-RAY DIFFRACTION51chain 'H' and (resid 134 through 165 )
52X-RAY DIFFRACTION52chain 'H' and (resid 166 through 207 )
53X-RAY DIFFRACTION53chain 'H' and (resid 208 through 223 )
54X-RAY DIFFRACTION54chain 'I' and (resid 3 through 38 )
55X-RAY DIFFRACTION55chain 'I' and (resid 39 through 86 )
56X-RAY DIFFRACTION56chain 'I' and (resid 87 through 100 )
57X-RAY DIFFRACTION57chain 'I' and (resid 101 through 119 )
58X-RAY DIFFRACTION58chain 'I' and (resid 120 through 133 )
59X-RAY DIFFRACTION59chain 'I' and (resid 134 through 165 )
60X-RAY DIFFRACTION60chain 'I' and (resid 166 through 207 )
61X-RAY DIFFRACTION61chain 'I' and (resid 208 through 223 )
62X-RAY DIFFRACTION62chain 'J' and (resid 3 through 38 )
63X-RAY DIFFRACTION63chain 'J' and (resid 39 through 86 )
64X-RAY DIFFRACTION64chain 'J' and (resid 87 through 133 )
65X-RAY DIFFRACTION65chain 'J' and (resid 134 through 165 )
66X-RAY DIFFRACTION66chain 'J' and (resid 166 through 207 )
67X-RAY DIFFRACTION67chain 'J' and (resid 208 through 223 )
68X-RAY DIFFRACTION68chain 'K' and (resid 3 through 38 )
69X-RAY DIFFRACTION69chain 'K' and (resid 39 through 86 )
70X-RAY DIFFRACTION70chain 'K' and (resid 87 through 133 )
71X-RAY DIFFRACTION71chain 'K' and (resid 134 through 165 )
72X-RAY DIFFRACTION72chain 'K' and (resid 166 through 223 )
73X-RAY DIFFRACTION73chain 'L' and (resid 3 through 38 )
74X-RAY DIFFRACTION74chain 'L' and (resid 39 through 86 )
75X-RAY DIFFRACTION75chain 'L' and (resid 87 through 100 )
76X-RAY DIFFRACTION76chain 'L' and (resid 101 through 133 )
77X-RAY DIFFRACTION77chain 'L' and (resid 134 through 165 )
78X-RAY DIFFRACTION78chain 'L' and (resid 166 through 207 )
79X-RAY DIFFRACTION79chain 'L' and (resid 208 through 223 )
80X-RAY DIFFRACTION80chain 'M' and (resid 3 through 38 )
81X-RAY DIFFRACTION81chain 'M' and (resid 39 through 86 )
82X-RAY DIFFRACTION82chain 'M' and (resid 87 through 133 )
83X-RAY DIFFRACTION83chain 'M' and (resid 134 through 165 )
84X-RAY DIFFRACTION84chain 'M' and (resid 166 through 207 )
85X-RAY DIFFRACTION85chain 'M' and (resid 208 through 223 )
86X-RAY DIFFRACTION86chain 'N' and (resid 3 through 38 )
87X-RAY DIFFRACTION87chain 'N' and (resid 39 through 86 )
88X-RAY DIFFRACTION88chain 'N' and (resid 87 through 100 )
89X-RAY DIFFRACTION89chain 'N' and (resid 101 through 119 )
90X-RAY DIFFRACTION90chain 'N' and (resid 120 through 133 )
91X-RAY DIFFRACTION91chain 'N' and (resid 134 through 165 )
92X-RAY DIFFRACTION92chain 'N' and (resid 166 through 207 )
93X-RAY DIFFRACTION93chain 'N' and (resid 208 through 223 )
94X-RAY DIFFRACTION94chain 'O' and (resid 3 through 38 )
95X-RAY DIFFRACTION95chain 'O' and (resid 39 through 86 )
96X-RAY DIFFRACTION96chain 'O' and (resid 87 through 133 )
97X-RAY DIFFRACTION97chain 'O' and (resid 134 through 165 )
98X-RAY DIFFRACTION98chain 'O' and (resid 166 through 207 )
99X-RAY DIFFRACTION99chain 'O' and (resid 208 through 223 )
100X-RAY DIFFRACTION100chain 'P' and (resid 3 through 38 )
101X-RAY DIFFRACTION101chain 'P' and (resid 39 through 86 )
102X-RAY DIFFRACTION102chain 'P' and (resid 87 through 100 )
103X-RAY DIFFRACTION103chain 'P' and (resid 101 through 119 )
104X-RAY DIFFRACTION104chain 'P' and (resid 120 through 133 )
105X-RAY DIFFRACTION105chain 'P' and (resid 134 through 151 )
106X-RAY DIFFRACTION106chain 'P' and (resid 152 through 165 )
107X-RAY DIFFRACTION107chain 'P' and (resid 166 through 207 )
108X-RAY DIFFRACTION108chain 'P' and (resid 208 through 223 )

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万見について

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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