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- PDB-5koi: Crystal Structure of a Possible Enoyl-(acyl-carrier-protein) Redu... -

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基本情報

登録情報
データベース: PDB / ID: 5koi
タイトルCrystal Structure of a Possible Enoyl-(acyl-carrier-protein) Reductase from Brucella melitensis
要素Enoyl-[acyl-carrier-protein] reductase [NADH]
キーワードOXIDOREDUCTASE / SSGCID / NAD / reductase / fatty acid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
機能・相同性
機能・相同性情報


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
類似検索 - 分子機能
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
類似検索 - 構成要素
生物種Brucella abortus biovar 1 (ウシ流産菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.7 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
引用ジャーナル: to be published
タイトル: Crystal Structure of a Possible Enoyl-(acyl-carrier-protein) Reductase from Brucella melitensis
著者: Dranow, D.M. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
履歴
登録2016年6月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年7月13日Provider: repository / タイプ: Initial release
改定 1.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)258,28116
ポリマ－252,9748
非ポリマー5,3078
水29,8331656
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,5704
ポリマ－63,2432
非ポリマー1,3272
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-30 kcal/mol
Surface area22930 Å2
手法PISA
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,5704
ポリマ－63,2432
非ポリマー1,3272
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-28 kcal/mol
Surface area22850 Å2
手法PISA
3
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,5704
ポリマ－63,2432
非ポリマー1,3272
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-28 kcal/mol
Surface area22740 Å2
手法PISA
4
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,5704
ポリマ－63,2432
非ポリマー1,3272
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-26 kcal/mol
Surface area23510 Å2
手法PISA
単位格子
Length a, b, c (Å)64.910, 83.830, 106.290
Angle α, β, γ (deg.)90.250, 100.080, 90.820
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Enoyl-[acyl-carrier-protein] reductase [NADH]


分子量: 31621.695 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Brucella abortus biovar 1 (strain 9-941) (ウシ流産菌)
株: 9-941 / 遺伝子: fabI-2, BruAb1_2144 / プラスミド: BrabA.00010.c.A1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q57A95, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / コメント: NAD*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1656 / 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: 2.25 Å3/Da / 溶媒含有率: 45.35 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: BrabA.00010.c.A1.PS000047 at 18.1 mg/ml, incubated with 4 mM NAD, protein mixed 1:1 and incubated with an equal volume PACT(a6): 25% (w/v) PEG-1500, 10 % (v/v) 10x SPG, pH=9, and ...詳細: BrabA.00010.c.A1.PS000047 at 18.1 mg/ml, incubated with 4 mM NAD, protein mixed 1:1 and incubated with an equal volume PACT(a6): 25% (w/v) PEG-1500, 10 % (v/v) 10x SPG, pH=9, and cryoprotected with 20% ethylene glycol

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2016年5月27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: 0.97949 Å / 相対比: 1
反射解像度: 1.7→50 Å / Num. obs: 236079 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / 冗長度: 3.9 % / Biso Wilson estimate: 19.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.19
反射 シェル

Diffraction-ID: 1

解像度 (Å)最高解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
1.7-1.7440.4742.910.89895.6
1.74-1.790.3823.570.92495.8
1.79-1.840.3134.320.94796.1
1.84-1.90.2355.60.96796.3
1.9-1.960.187.030.98296.4
1.96-2.030.1448.660.98796.6
2.03-2.110.1210.360.98996.9
2.11-2.190.09812.560.99197.2
2.19-2.290.08314.480.99397.4
2.29-2.40.07416.010.99497.6
2.4-2.530.06517.680.99597.8
2.53-2.690.05819.970.99598.1
2.69-2.870.05321.860.99698.3
2.87-3.10.04624.360.99798.4
3.1-3.40.041270.99798.6
3.4-3.80.03928.990.99798.9
3.8-4.390.03431.110.99899
4.39-5.380.03331.390.99899.4
5.38-7.60.03430.940.99899.6
7.60.03332.920.99799.3

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHASER位相決定
PHENIX精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3GRK

3grk


解像度: 1.7→48.675 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 2.04 / 位相誤差: 16.75
Rfactor反射数%反射
Rfree0.1756 11802 5 %
Rwork0.1465 --
obs0.148 236058 97.26 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 91.3 Å2 / Biso mean: 25.2716 Å2 / Biso min: 9.44 Å2
精密化ステップサイクル: final / 解像度: 1.7→48.675 Å
タンパク質核酸リガンド溶媒全体
原子数16065 0 572 1677 18314
Biso mean--29.66 34.39 -
残基数----2158
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00617437
X-RAY DIFFRACTIONf_angle_d0.83523833
X-RAY DIFFRACTIONf_chiral_restr0.0532724
X-RAY DIFFRACTIONf_plane_restr0.0053334
X-RAY DIFFRACTIONf_dihedral_angle_d14.47710677
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.25283880.21667375776395
1.7193-1.73950.24713830.21737286766996
1.7395-1.76070.23893900.20147400779096
1.7607-1.7830.25753880.20017371775996
1.783-1.80650.22393900.19017415780596
1.8065-1.83120.23243840.19497303768796
1.8312-1.85740.22273910.18077419781096
1.8574-1.88510.20323880.1737381776996
1.8851-1.91460.21693910.17087419781096
1.9146-1.9460.20633900.16247423781396
1.946-1.97950.2143890.16027391778097
1.9795-2.01550.19193930.14977454784797
2.0155-2.05430.18973910.1517440783197
2.0543-2.09620.19733940.15357471786597
2.0962-2.14180.16823900.14537417780797
2.1418-2.19160.18483950.1467510790597
2.1916-2.24640.18373940.14677472786697
2.2464-2.30710.18383940.13797486788097
2.3071-2.3750.17643940.13977493788798
2.375-2.45170.17693940.14177495788998
2.4517-2.53930.18833980.14627556795498
2.5393-2.6410.17153960.1397517791398
2.641-2.76120.18213960.14717527792398
2.7612-2.90670.20113980.15267562796098
2.9067-3.08880.18264010.15147629803099
3.0888-3.32720.16143970.14477536793399
3.3272-3.6620.16324010.14157623802499
3.662-4.19160.13644010.12187607800899
4.1916-5.280.13314020.11737643804599
5.28-48.69470.1524010.1447635803699
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)
13.45270.1940.42192.170.28214.8769-0.21050.16490.3321-0.04160.04710.0277-0.52630.20770.10230.2835-0.0165-0.04060.07010.03940.2401-7.499560.92030.0015
22.3272-0.28940.11071.9070.53684.8361-0.01740.17130.2362-0.0453-0.03-0.0033-0.2967-0.03020.06670.2512-0.0024-0.0370.10380.04140.2293-9.336561.4178-2.3819
34.4729-0.9143-0.68759.9075.19012.7327-0.28650.34510.2961-0.1152-0.13880.4678-0.842-0.13610.37830.3411-0.0132-0.09310.20670.0890.3166-13.315366.0725-11.5066
41.29280.25830.24135.73392.30613.4443-0.10660.31780.0928-0.36340.042-0.3913-0.39520.48710.05940.281-0.0703-0.00270.27160.11830.23380.905860.3054-12.9855
51.45180.81590.78672.12980.90761.2537-0.03780.23480.0871-0.11730.0289-0.0716-0.16560.12430.0240.1831-0.02460.00010.19560.03780.112-5.429645.1399-11.7132
62.49490.44740.77220.83510.14371.3558-0.0590.10580.1601-0.07030.01410.0383-0.09840.03350.06390.1395-0.01050.00470.11910.01080.1152-7.102343.4104-2.3762
72.33971.1415-0.45042.40320.40952.15770.00590.10390.2878-0.1622-0.0490.1472-0.1268-0.15110.11780.15560.0248-0.01490.1729-0.00550.2269-26.800943.29832.5014
82.29810.83160.32781.10220.23340.82470.0164-0.00660.10270.033-0.0510.0053-0.1176-0.00210.03660.1657-0.0032-0.00710.1333-0.00120.1455-12.223246.28927.6569
97.71894.843.96399.44465.35559.0876-0.0525-0.103-0.0925-0.0632-0.16350.1497-0.2031-0.41390.20090.09690.00960.02740.20530.0030.1753-36.543429.11483.6043
103.98130.5798-1.72541.5757-0.73784.4867-0.0255-0.006-0.2843-0.0580.00910.04370.4031-0.135-0.01380.2122-0.0483-0.02620.08020.00580.2507-15.02210.807612.934
115.3199-0.6713-3.75983.21462.02478.4046-0.149-0.2468-0.5302-0.2420.11830.43210.381-0.51720.02710.2954-0.0816-0.04140.24950.07740.3789-24.8274-3.344119.6118
121.1763-0.27690.06731.18770.08280.82640.0165-0.1145-0.21470.1594-0.01480.04560.1484-0.0639-0.00140.1613-0.03780.01210.15440.02010.1865-14.384813.348822.5894
131.3241-0.4169-0.06961.21780.21.046-0.0232-0.0057-0.13490.05110.01110.14120.0739-0.0928-0.03120.1451-0.03330.00890.12320.01520.1619-12.455718.279715.252
143.0734-1.59110.79311.5256-0.18770.6150.0830.0335-0.1126-0.0407-0.06750.08710.0761-0.0571-0.0160.1331-0.01510.00550.1396-0.01860.1501-18.738517.64492.7618
154.4453-2.5987-0.55722.70040.94757.6033-0.22180.1380.2135-0.3385-0.0620.5792-0.1501-0.62670.2690.1809-0.0021-0.06120.26120.00230.2638-34.279636.1838-3.8635
162.895-0.2262-0.20242.7737-0.04242.88710.16460.4009-0.3081-0.13830.01910.05750.42060.2473-0.07220.22450.0465-0.03770.1999-0.11430.2121-2.42118.3662-13.9722
172.4151-0.4639-1.07662.77840.08962.60510.17080.3949-0.281-0.3031-0.0405-0.31620.31250.5212-0.03880.19240.06120.0090.3508-0.12770.25233.50579.2042-17.0153
180.95190.01530.0414.49330.07552.08240.16630.4805-0.1545-0.6013-0.0674-0.04030.14040.0802-0.11520.32060.02420.00460.4266-0.14120.1907-3.772716.8191-26.8962
191.60720.83130.54422.3920.53970.8295-0.04620.4392-0.2405-0.25580.1665-0.1989-0.05480.2775-0.09890.1725-0.00060.01730.2979-0.05560.15581.200123.4956-14.4406
201.34550.67150.45391.57860.27311.260.02410.1684-0.0645-0.1117-0.0129-0.0237-0.01260.1013-0.02160.12670.01380.0250.2175-0.02740.1393-2.023628.8089-11.7116
212.19530.74160.45061.23770.269810.0280.1103-0.1085-0.0440.0111-0.09210.00070.1139-0.03210.14660.01460.010.1786-0.03390.1254-5.789824.9196-7.3112
221.5970.40440.6710.64150.27980.69660.04990.0811-0.172-0.00810.0195-0.12290.07120.1201-0.08620.12690.01090.00240.1555-0.01760.16423.005716.02821.3892
231.7316-0.351.56282.01330.27443.6902-0.12350.02250.290.1864-0.0404-0.054-0.16770.28490.13650.1584-0.01280.00670.17050.00410.15549.21525.691312.1775
242.91340.23221.2222.3142-1.10374.43520.0512-0.16090.1010.0548-0.05880.0695-0.2987-0.0583-0.00740.1942-0.0085-0.01120.1085-0.07430.1499-8.587252.621529.3285
254.07932.2905-1.95039.1883-6.46814.6033-0.0157-0.4064-0.21640.3117-0.1445-0.76510.0703-0.23430.1730.291-0.0367-0.08140.2154-0.05230.2053-3.907352.025340.1185
261.9861-0.54-0.68888.7066-0.64132.7921-0.0066-0.3484-0.01840.5868-0.04520.4539-0.0715-0.28280.05090.2267-0.01250.03140.3085-0.09190.1779-18.248345.710738.7214
271.9025-1.48360.30623.48820.00910.9753-0.036-0.20720.05090.1898-0.0108-0.0435-0.0148-0.06280.04690.1338-0.02430.01410.1663-0.00560.0921-11.172233.164229.9023
281.5689-0.6550.37891.4592-0.10641.1914-0.0348-0.07710.16140.0901-0.02-0.1632-0.03930.01590.05460.1404-0.01570.01090.1267-0.01570.1367-9.029137.331320.56
295.5111-1.4936-1.32265.8448-2.86412.29380.1438-0.41820.06940.3504-0.0049-0.3163-0.08680.0876-0.10840.2113-0.0371-0.05220.2112-0.02150.203112.243935.35319.3347
302.9895-0.9091-0.38270.59620.15430.67660.00220.00330.07220.0212-0.0329-0.044-0.08260.08540.02990.1562-0.0223-0.00920.11520.00310.1511-2.0544.563114.0383
318.7-4.88370.40029.9654-0.47175.3526-0.04310.0914-0.10290.01280.0018-0.208-0.09240.12390.04910.1284-0.02340.01210.26260.00060.183220.100127.85128.2165
323.4914-1.19280.32023.41-0.76853.6331-0.1284-0.10990.3871-0.12320.01890.0291-0.4594-0.16170.10220.29710.0144-0.08520.0702-0.05070.300613.6043101.948163.8472
332.1093-0.0302-0.09192.8434-2.08944.723-0.0396-0.27430.297-0.03830.01610.0264-0.4346-0.08290.01170.28250.0013-0.08740.1122-0.06680.312515.9355102.135666.388
344.52412.3799-2.33927.4057-5.21663.81160.0913-0.48420.47460.1558-0.130.0532-0.9320.56350.07020.35620.0173-0.1030.2413-0.12050.34819.7417107.008975.5926
351.4458-0.1648-0.05394.153-0.96512.0606-0.1034-0.35610.3670.2488-0.04410.4167-0.4399-0.25750.12230.33280.0864-0.05060.2842-0.14770.33335.6827100.976277.0205
361.1835-0.47340.64872.227-0.62341.3775-0.0765-0.2830.15650.15990.049-0.0051-0.1165-0.12770.03310.17960.0326-0.00480.2188-0.06250.139512.285485.965775.9521
372.2909-0.22680.57891.7189-0.13671.9371-0.0208-0.03340.06580.0316-0.0110.0156-0.05810.01250.0420.1329-0.0047-00.143-0.02350.128215.947183.652565.711
383.2348-0.26411.71331.1997-0.33272.5577-0.1188-0.21490.24260.08720.01130.0527-0.1678-0.13940.0630.15240.0140.01470.1582-0.02840.15117.531381.733966.9466
391.7155-0.85020.64681.5758-0.00461.5661-0.1994-0.19950.21790.23820.1464-0.2526-0.14950.05710.10540.18360.0215-0.03240.1293-0.04180.201920.839987.936467.1217
401.9586-0.76070.47061.0742-0.06790.637-0.0519-0.01720.22890.0279-0.0162-0.1606-0.09650.07260.08130.1626-0.0174-0.01320.1330.00830.195924.341285.874858.2404
419.3882-4.00852.39898.7443-2.20516.88640.0725-0.39860.01970.07620.033-0.1931-0.17640.2296-0.07360.1251-0.01570.02190.2772-0.00370.226943.652669.743961.2979
424.2796-0.7748-0.44563.1594-0.23823.49210.15890.1677-0.18030.01730.0670.02740.46820.1884-0.18660.26570.0692-0.04110.1047-0.03240.250922.499541.394951.8665
432.7796-2.31760.9557.7417-2.59533.25730.24640.3663-0.3519-0.0689-0.1791-0.42510.49250.4383-0.0350.38420.1267-0.0230.2638-0.09550.378228.080439.581942.5828
441.55241.9429-2.46174.24-4.77775.50060.20370.4361-0.2842-0.5880.0520.55350.6738-0.1013-0.14460.42110.0702-0.07950.226-0.10060.342215.43640.488436.8126
451.8530.7906-0.09741.9458-0.2611.09050.05130.1785-0.0758-0.08380.0017-0.06990.12830.1306-0.03590.14830.02790.01610.1683-0.02180.155223.42958.133140.2774
461.10291.79720.59343.93770.59521.28630.0484-0.1138-0.03810.0549-0.05380.13090.1156-0.0329-0.00110.13560.01480.00650.15010.00260.161220.904259.295551.4529
471.16930.47060.17210.931-0.1791.12670.00340.0705-0.1825-0.0733-0.019-0.20110.08250.1245-0.04110.14420.01450.01120.1084-0.00670.174519.997658.443749.2453
481.44990.34690.4540.57170.1550.67730.0649-0.0241-0.03480.0239-0.0189-0.0810.08070.0684-0.02370.14320.0045-0.00250.150.02170.16125.954758.366961.7711
495.34214.9184-0.58187.768-2.38236.7664-0.2116-0.06520.40410.1141-0.083-0.4963-0.37250.75560.28380.2136-0.0119-0.10130.3168-0.00220.373641.466877.452967.8018
501.8851.0716-0.23792.606-0.33733.03390.2681-0.669-0.28390.2959-0.07920.05070.3184-0.55620.010.2502-0.0839-0.01630.40920.13270.22246.322649.512980.7944
511.151-0.20820.43721.3283-0.19691.1530.0062-0.3866-0.10270.23790.05570.05280.0552-0.1923-0.03970.1663-0.00640.01770.32050.03350.12538.798265.675380.4568
520.6146-0.5402-0.00181.2417-0.21460.9501-0.0525-0.2087-0.08710.07060.08330.1497-0.0259-0.2017-0.02560.1186-0.01230.00530.19170.03910.108810.231465.296571.7333
532.6502-0.74640.9380.7301-0.20891.05530.0556-0.1607-0.14090.00790.01310.08340.087-0.1131-0.07250.1081-0.02210.0070.11460.01730.12274.835458.379861.5374
542.3608-1.78161.25116.9155-2.52881.9611-0.07660.03550.3691-0.35530.12810.90150.0243-0.77730.04840.2201-0.0373-0.06330.33060.00920.2989-11.175370.380746.0391
552.1843-0.26490.55242.58180.96983.19790.08220.25470.2907-0.0972-0.0177-0.1195-0.3318-0.0001-0.07520.2379-0.00310.00530.14170.11650.248915.241592.742334.7713
561.5351-0.3256-0.54522.8877-0.38071.57450.15470.48510.1988-0.5215-0.1761-0.0502-0.03080.07570.01030.30690.02820.03380.3290.12850.244519.416787.721524.7702
571.72431.2290.0843.7645-0.00220.61960.01760.19240.0863-0.1822-0.0443-0.0794-0.06840.03180.02550.1508-0.00150.01520.16190.03630.096118.348673.452934.4317
581.23940.18870.22911.2747-0.0681.2193-0.07260.16670.2061-0.13490.0260.0116-0.0910.03620.03850.1308-0.00690.01070.10820.03020.137816.122877.750543.3846
593.25951.3897-0.16121.3436-0.28340.4257-0.029-0.02190.1179-0.01250.00360.0734-0.0677-0.07380.02890.14860.01420.00160.1194-0.00110.15131.917679.843250.1511
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )A21 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 56 )A43 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 82 )A57 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 135 )A83 - 135
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 203 )A136 - 203
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 222 )A204 - 222
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 259 )A223 - 259
9X-RAY DIFFRACTION9chain 'A' and (resid 260 through 272 )A260 - 272
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 42 )B2 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 56 )B43 - 56
12X-RAY DIFFRACTION12chain 'B' and (resid 57 through 157 )B57 - 157
13X-RAY DIFFRACTION13chain 'B' and (resid 158 through 203 )B158 - 203
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 259 )B204 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 272 )B260 - 272
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 20 )C2 - 20
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 56 )C21 - 56
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 82 )C57 - 82
19X-RAY DIFFRACTION19chain 'C' and (resid 83 through 104 )C83 - 104
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 157 )C105 - 157
21X-RAY DIFFRACTION21chain 'C' and (resid 158 through 203 )C158 - 203
22X-RAY DIFFRACTION22chain 'C' and (resid 204 through 244 )C204 - 244
23X-RAY DIFFRACTION23chain 'C' and (resid 245 through 270 )C245 - 270
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 42 )D2 - 42
25X-RAY DIFFRACTION25chain 'D' and (resid 43 through 56 )D43 - 56
26X-RAY DIFFRACTION26chain 'D' and (resid 57 through 82 )D57 - 82
27X-RAY DIFFRACTION27chain 'D' and (resid 83 through 135 )D83 - 135
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 201 )D136 - 201
29X-RAY DIFFRACTION29chain 'D' and (resid 202 through 214 )D202 - 214
30X-RAY DIFFRACTION30chain 'D' and (resid 215 through 259 )D215 - 259
31X-RAY DIFFRACTION31chain 'D' and (resid 260 through 272 )D260 - 272
32X-RAY DIFFRACTION32chain 'E' and (resid 2 through 20 )E2 - 20
33X-RAY DIFFRACTION33chain 'E' and (resid 21 through 42 )E21 - 42
34X-RAY DIFFRACTION34chain 'E' and (resid 43 through 56 )E43 - 56
35X-RAY DIFFRACTION35chain 'E' and (resid 57 through 82 )E57 - 82
36X-RAY DIFFRACTION36chain 'E' and (resid 83 through 135 )E83 - 135
37X-RAY DIFFRACTION37chain 'E' and (resid 136 through 157 )E136 - 157
38X-RAY DIFFRACTION38chain 'E' and (resid 158 through 181 )E158 - 181
39X-RAY DIFFRACTION39chain 'E' and (resid 182 through 203 )E182 - 203
40X-RAY DIFFRACTION40chain 'E' and (resid 204 through 259 )E204 - 259
41X-RAY DIFFRACTION41chain 'E' and (resid 260 through 272 )E260 - 272
42X-RAY DIFFRACTION42chain 'F' and (resid 2 through 42 )F2 - 42
43X-RAY DIFFRACTION43chain 'F' and (resid 43 through 68 )F43 - 68
44X-RAY DIFFRACTION44chain 'F' and (resid 69 through 83 )F69 - 83
45X-RAY DIFFRACTION45chain 'F' and (resid 84 through 135 )F84 - 135
46X-RAY DIFFRACTION46chain 'F' and (resid 136 through 157 )F136 - 157
47X-RAY DIFFRACTION47chain 'F' and (resid 158 through 203 )F158 - 203
48X-RAY DIFFRACTION48chain 'F' and (resid 204 through 259 )F204 - 259
49X-RAY DIFFRACTION49chain 'F' and (resid 260 through 272 )F260 - 272
50X-RAY DIFFRACTION50chain 'G' and (resid 2 through 56 )G2 - 56
51X-RAY DIFFRACTION51chain 'G' and (resid 57 through 157 )G57 - 157
52X-RAY DIFFRACTION52chain 'G' and (resid 158 through 203 )G158 - 203
53X-RAY DIFFRACTION53chain 'G' and (resid 204 through 259 )G204 - 259
54X-RAY DIFFRACTION54chain 'G' and (resid 260 through 272 )G260 - 272
55X-RAY DIFFRACTION55chain 'H' and (resid 2 through 42 )H2 - 42
56X-RAY DIFFRACTION56chain 'H' and (resid 43 through 82 )H43 - 82
57X-RAY DIFFRACTION57chain 'H' and (resid 83 through 135 )H83 - 135
58X-RAY DIFFRACTION58chain 'H' and (resid 136 through 201 )H136 - 201
59X-RAY DIFFRACTION59chain 'H' and (resid 202 through 272 )H202 - 272

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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://pdbjlvh1.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