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- PDB-5i7f: Crystal structure of B. pseudomallei FabI in complex with NAD and... -

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データを開く


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: 5i7f
タイトルCrystal structure of B. pseudomallei FabI in complex with NAD and PT405
要素Enoyl-[acyl-carrier-protein] reductase [NADH]
キーワードOXIDOREDUCTASE / enoyl-ACP reductase / diphenyl ethers / Burkholderia pseudomallei / slow binding inhibitors
機能・相同性
機能・相同性情報


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
5-ethyl-4-fluoro-2-(2-fluorophenoxy)phenol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
類似検索 - 構成要素
生物種Burkholderia pseudomallei (類鼻疽菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Eltschkner, S. / Tonge, P.J. / Kisker, C.
資金援助 ドイツ, 1件
組織認可番号
German Research FoundationSFB 630 ドイツ
引用ジャーナル: Biochemistry / : 2017
タイトル: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
著者: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
履歴
登録2016年2月17日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02017年2月22日Provider: repository / タイプ: Initial release
改定 1.12017年3月15日Group: Database references
改定 1.22017年4月19日Group: Database references
改定 1.32017年9月6日Group: Advisory / Author supporting evidence / Data collection
カテゴリ: diffrn_radiation_wavelength / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization
改定 1.42024年1月10日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: 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)362,86936
ポリマ-351,90512
非ポリマー10,96424
4,197233
1
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: 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)120,95612
ポリマ-117,3024
非ポリマー3,6558
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-144 kcal/mol
Surface area30160 Å2
手法PISA
2
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: 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)120,95612
ポリマ-117,3024
非ポリマー3,6558
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-144 kcal/mol
Surface area30530 Å2
手法PISA
3
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: 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)120,95612
ポリマ-117,3024
非ポリマー3,6558
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-144 kcal/mol
Surface area31040 Å2
手法PISA
単位格子
Length a, b, c (Å)138.434, 109.775, 269.802
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number5
Space group name H-MI121

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要素

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


分子量: 29325.391 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Burkholderia pseudomallei (類鼻疽菌)
遺伝子: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745
発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 12 / 由来タイプ: 合成 / : C21H27N7O14P2 / コメント: NAD*YM
#3: 化合物
ChemComp-68O / 5-ethyl-4-fluoro-2-(2-fluorophenoxy)phenol


分子量: 250.241 Da / 分子数: 12 / 由来タイプ: 合成 / : C14H12F2O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 233 / 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: 2.98 Å3/Da / 溶媒含有率: 58.72 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M Bistris, pH 6.5 20 % PEG 400

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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: ESRF / ビームライン: ID29 / 波長: 0.976 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2014年11月24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: 0.976 Å / 相対比: 1
反射解像度: 2.7→48.99 Å / Num. obs: 101650 / % possible obs: 94.8 % / 冗長度: 2.4 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.9
反射 シェル解像度: 2.7→2.73 Å / 冗長度: 2.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.4 / % possible all: 95.7

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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
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 4BKU
解像度: 2.7→47.171 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 24.82
Rfactor反射数%反射
Rfree0.223 4931 4.86 %
Rwork0.1917 --
obs0.1933 101481 94.4 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.7→47.171 Å
タンパク質核酸リガンド溶媒全体
原子数22944 0 744 233 23921
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00524177
X-RAY DIFFRACTIONf_angle_d0.93232810
X-RAY DIFFRACTIONf_dihedral_angle_d12.1118606
X-RAY DIFFRACTIONf_chiral_restr0.0343749
X-RAY DIFFRACTIONf_plane_restr0.0044411
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.36371700.32033215X-RAY DIFFRACTION95
2.7307-2.76280.37241630.31453249X-RAY DIFFRACTION96
2.7628-2.79650.34451700.30183231X-RAY DIFFRACTION96
2.7965-2.83190.3371840.30853247X-RAY DIFFRACTION96
2.8319-2.86910.32311640.29393261X-RAY DIFFRACTION96
2.8691-2.90840.31751850.2983218X-RAY DIFFRACTION96
2.9084-2.950.32661410.28483288X-RAY DIFFRACTION96
2.95-2.9940.32031740.27613236X-RAY DIFFRACTION96
2.994-3.04080.27461580.263254X-RAY DIFFRACTION95
3.0408-3.09060.27841570.2633198X-RAY DIFFRACTION94
3.0906-3.14390.27231730.25443156X-RAY DIFFRACTION93
3.1439-3.20110.29561710.2583230X-RAY DIFFRACTION95
3.2011-3.26260.29581750.25413226X-RAY DIFFRACTION96
3.2626-3.32920.2882050.23673259X-RAY DIFFRACTION96
3.3292-3.40160.27381580.22163233X-RAY DIFFRACTION96
3.4016-3.48070.23671580.22083198X-RAY DIFFRACTION94
3.4807-3.56770.24741510.20553240X-RAY DIFFRACTION95
3.5677-3.66410.24441720.20333228X-RAY DIFFRACTION94
3.6641-3.77190.21841620.18653207X-RAY DIFFRACTION94
3.7719-3.89360.21091380.17373128X-RAY DIFFRACTION92
3.8936-4.03270.1711640.16623195X-RAY DIFFRACTION94
4.0327-4.1940.17691700.14683248X-RAY DIFFRACTION94
4.194-4.38480.15941520.13643236X-RAY DIFFRACTION94
4.3848-4.61580.16781630.13543203X-RAY DIFFRACTION94
4.6158-4.90470.13811590.13353223X-RAY DIFFRACTION94
4.9047-5.28290.17151720.13663152X-RAY DIFFRACTION93
5.2829-5.81370.17831450.14643308X-RAY DIFFRACTION95
5.8137-6.6530.2021720.16743222X-RAY DIFFRACTION94
6.653-8.37440.17181560.14623174X-RAY DIFFRACTION92
8.3744-47.17810.18481490.1483087X-RAY DIFFRACTION87
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)
16.3570.0238-0.88382.55320.12028.62970.01590.77820.4554-0.1016-0.072-0.224-0.3790.23780.03610.54260.0398-0.10450.36780.05050.5476-2.245746.9921298.5304
22.5193-1.3864-2.04927.05843.86143.27640.05050.46540.3402-0.7114-0.24010.2765-0.8971-1.03090.17240.55920.0029-0.04210.71880.12580.6271-4.427647.3633294.7586
33.16370.681-0.16715.98231.20582.2580.17030.65250.7948-0.6878-0.061-0.123-0.1169-0.1645-0.12670.65150.04150.08130.69510.17130.70571.248844.6121288.7345
42.25560.13732.38376.5542-0.92055.4568-0.0579-0.52020.4057-1.35940.80790.91350.2460.3997-0.30820.7995-0.1068-0.06350.8644-0.15240.7417-12.341917.0955290.8
52.38851.0584-1.28693.6193-0.77273.1305-0.01020.41140.4543-0.3380.0901-0.05430.1148-0.1029-0.11310.4810.0120.04990.48690.0160.56571.426829.9722295.8619
63.854-1.71960.84462.1044-0.67892.00580.24420.23420.162-0.2064-0.1204-0.07240.2636-0.0427-0.10290.472-0.01050.0660.48630.01530.4927-0.72430.3674300.5628
74.64811.1768-2.16542.8251-0.78992.07630.04070.25560.2272-0.06180.01090.2139-0.0171-0.2657-0.07640.46460.0258-0.04190.5355-0.01580.4995-9.235934.143310.394
84.6555-1.0132-0.17824.599-2.81057.88550.1518-0.56060.14130.52390.0737-0.5755-0.36670.4108-0.06110.6358-0.0018-0.13730.5344-0.21040.80313.162347.276330.6037
91.3255-1.6871-0.67643.99730.87464.3254-0.2779-0.76180.56660.36990.3055-0.463-0.44810.01810.01130.72250.0696-0.12750.7253-0.23690.6822-1.387944.1821338.2128
101.6182-1.4597-1.47264.05070.13691.4591-0.2956-0.61640.21540.60450.2315-0.4764-0.01820.15470.13710.52830.0316-0.14350.7026-0.09890.54242.487927.5262331.9815
110.3608-0.1908-0.95751.88060.18961.8784-0.0459-0.220.20840.1740.0555-0.434-0.03810.23140.02640.47310.009-0.04820.5931-0.05370.61215.524233.6083322.0216
122.2048-1.62941.3362.85581.43266.21380.43450.25370.9825-0.0833-0.2142-1.1260.1555-0.0367-0.23150.4257-0.10270.0360.4992-0.01390.702411.316428.6885313.6635
132.93991.28290.60721.6837-0.88263.51470.29180.4832-0.4404-0.2494-0.1155-0.16340.33310.1731-0.15210.71840.01110.23030.5621-0.10680.81726.7968-5.8244298.2913
148.23612.9053-1.07637.83680.25167.6955-0.09511.4398-0.6386-0.1380.2602-0.5517-0.1506-0.0227-0.40350.9518-0.00520.30050.6712-0.09350.911214.36-6.5187287.198
152.3370.48940.5173.0289-1.82311.4651-0.06580.5509-0.4722-0.8428-0.03480.14910.2246-0.32780.05760.9191-0.07080.16020.7211-0.19180.68381.313-1.1227288.5094
160.2915-0.13430.98753.66221.14242.38510.02190.1304-0.1377-0.384-0.1355-0.22470.09180.14650.11660.57-0.03030.14430.5635-0.11070.645.780514.5817295.1536
171.7431-2.3373-1.05533.36550.56791.62670.08740.17710.1038-0.1033-0.1778-0.23040.075-0.06290.09590.5682-0.0320.05810.4691-0.04820.47924.255911.4188300.7376
183.15432.09241.71042.14580.51093.1885-0.0532-0.1231-0.1882-0.1127-0.0304-0.56430.01790.07830.05970.5390.07210.11890.50040.01140.706611.367.4642311.664
195.0485-0.68840.12284.18820.59065.2813-0.4299-1.0873-0.70320.05640.22680.1110.48030.49840.2490.71540.04490.24650.51780.12030.759-2.247-5.5928327.7198
203.13710.77560.66597.16670.72633.2783-0.2074-0.6856-0.56470.76560.10920.54020.2866-0.2417-0.00060.65460.06550.14170.6980.19720.7465-5.162-6.3618334.6186
212.7816-3.26752.23617.1269-1.72735.989-0.1068-0.4253-0.42730.80230.1289-0.23270.03330.8078-0.04680.53880.06770.03920.8470.1430.63643.82620.0558337.5052
223.3886-3.41910.33664.5123-0.46721.9033-0.3416-0.5911-0.36670.57270.42090.1876-0.0398-0.3494-0.01640.6450.05870.03780.73850.05570.567-4.193316.0573336.0537
230.79091.30270.30223.7144-0.71962.9572-0.0716-0.1247-0.23710.1201-0.0533-0.14410.1793-0.05380.11840.4271-0.0240.03640.497-0.00160.46580.22912.7416325.4079
240.24710.20350.37251.718-0.13431.7716-0.0595-0.0135-0.13320.0443-0.02020.1842-0.063-0.18440.04130.5101-0.03050.09840.57-0.02470.6325-7.78076.8642317.8231
255.3141-0.30631.24883.42141.05415.8225-0.37330.48430.7737-0.55770.02820.2465-0.34080.22890.33070.6457-0.0003-0.08760.30240.03750.6285-70.846547.0112298.171
262.7968-1.8113-1.40873.98450.08393.37960.05750.58360.6151-1.05970.02860.6303-0.1757-0.6078-0.23450.8737-0.0542-0.15170.56780.19690.7287-73.30747.6912291.0653
270.7540.1221-0.71684.88860.340.77850.01240.33430.2123-1.02290.09010.3437-0.1644-0.0869-0.18840.871-0.0025-0.12520.68530.12010.4507-69.148334.4696289.5897
282.32130.117-0.12333.5017-0.8160.9372-0.36870.42620.2878-0.97850.38980.25090.0731-0.1232-0.12440.8588-0.06240.01530.53080.05760.3937-65.294429.1578289.2502
293.13633.1986-2.86067.3573-1.40652.43390.34370.50780.50790.30310.08280.2415-0.0987-0.0833-0.35730.47910.0071-0.16160.48890.05610.477-69.813330.8972302.055
301.3574-0.2778-0.05262.44950.07211.44010.0026-0.00640.113-0.3567-0.03670.3811-0.0074-0.12970.03060.44130.0066-0.08640.44570.04820.5078-73.550932.5235305.938
315.45711.02311.8982.9942-2.0698.01310.2421-0.49740.58950.10740.13730.1166-0.4569-0.1527-0.27780.4849-0.06870.06980.4334-0.13410.579-64.296146.9786327.5472
322.8308-0.9898-2.00438.8964-4.68635.01690.1024-0.30630.23880.5824-0.0567-0.1457-0.40650.36870.05770.4787-0.085-0.03190.5095-0.20360.5753-61.956347.6039330.9296
331.6455-0.6435-0.08145.0705-1.02430.71350.2196-0.51340.47570.9005-0.18280.2431-0.14180.1542-0.02740.7075-0.07620.10270.6523-0.19010.6197-66.92344.0925337.633
341.3908-0.7488-1.82834.1225-0.11691.47680.0014-0.42390.05050.65670.0137-0.1765-0.10550.3527-0.02090.4299-0.0409-0.11890.5489-0.04080.455-63.291827.2285331.2319
353.9317-1.39761.94933.1192-0.07951.7184-0.31050.5198-0.49420.18520.1178-0.0317-0.09260.10620.13450.4514-0.03950.03230.4956-0.02060.4351-69.244826.3187326.2882
360.4170.2747-0.51052.91960.59752.18730.0949-0.120.2250.02650.0549-0.3183-0.02110.2186-0.11280.358-0.0188-0.05220.4689-0.01020.4983-58.201134.6147317.8513
373.9191.39641.35734.26861.57623.4812-0.64840.8257-0.5593-0.61590.3488-0.13530.3774-0.2580.21590.60530.04480.07220.49750.0670.54-62.6935-5.177297.7005
380.63970.13690.37336.0534-0.13361.51280.01370.4099-0.3701-1.28080.0649-0.07020.20490.1183-0.10120.8417-0.05450.03330.5911-0.09750.5484-63.7614-3.6248289.8616
391.87890.69171.3737.8852-0.67693.058-0.35910.4032-0.726-0.990.0375-1.32960.7148-0.21580.21110.8942-0.09970.22640.69620.05120.7064-52.065624.6104291.1383
401.1420.65090.19894.20780.08581.8062-0.07560.0689-0.0321-0.79430.13240.08960.0196-0.0086-0.05550.57990.0023-0.05170.48290.00770.3679-67.024812.7508296.2978
411.0811-0.23830.55881.97911.07452.0238-0.0135-0.2421-0.0835-0.32780.1018-0.3082-0.03830.1918-0.09040.46650.01690.00120.45210.04860.4925-57.4017.5895307.4084
422.5066-0.62870.10334.0631.30642.602-0.0106-0.5229-0.39540.26990.09880.0820.1462-0.0165-0.0670.4561-0.0485-0.03740.56420.14860.4539-68.649-5.5417327.1169
431.92770.57171.20783.96521.25653.02330.1057-0.6476-0.47940.5926-0.07260.31270.2795-0.20860.00660.5765-0.0351-0.00450.64580.2030.6161-70.9189-6.2759334.3622
441.67320.5182-0.20133.3549-0.46740.69570.1397-0.6346-0.37370.5532-0.0638-0.3520.0681-0.1674-0.09610.63610.0017-0.07230.69140.16340.5218-61.7420.0021336.3682
454.6969-2.71510.30629.05732.44643.39920.0761-0.78780.35411.15340.32550.7814-0.0309-1.1408-0.47370.616-0.02990.10820.84910.01180.6041-81.398522.9772334.597
461.1127-0.87880.33333.20610.28380.7741-0.0126-0.3651-0.09560.487-0.0212-0.00910.09980.03740.01260.4224-0.028-0.01820.53430.08780.4737-66.370611.6464330.2237
473.06890.1885-1.47144.5580.9192.6998-0.1213-0.43270.02990.19730.0765-0.05940.03330.34190.00430.3837-0.0174-0.07830.4920.08230.4092-62.32814.3294326.0036
480.18040.54810.13981.908-0.25281.4903-0.0229-0.0208-0.13590.07890.04640.33570.0459-0.4145-0.04610.35730.0064-0.02720.52870.06380.4929-75.59876.9502317.5999
493.44630.6561.36957.0653-0.28210.8567-0.21780.2086-0.4811-0.7504-0.1364-0.40290.0064-0.13710.34010.7047-0.03250.08920.617-0.02350.4004-36.55416.2483234.2954
502.62970.01830.19346.0892-2.2084.1145-0.28630.3228-0.5685-0.5243-0.05180.09650.3917-0.41930.42090.6907-0.02450.07370.6237-0.15710.6043-36.4207-2.5214234.8028
511.3072-0.3714-1.54742.56990.18752.7929-0.15870.1325-0.2671-0.1381-0.08820.00020.3178-0.13670.27450.4982-0.04870.02780.5856-0.01610.5526-35.34321.9843251.0858
522.56571.4859-0.01633.0087-1.04511.1456-0.0129-0.0244-0.15430.0255-0.2202-0.0861-0.0496-0.02460.21330.5144-0.00350.02650.5504-0.08470.4778-35.17088.014251.0389
532.7021-0.1427-0.42372.6627-0.23441.7521-0.06260.17310.0216-0.0258-0.01280.33870.1009-0.18860.06890.5354-0.0291-0.05950.5945-0.03020.4597-42.96918.5012246.9769
543.99881.1969-1.25137.86631.84852.9528-0.12240.3230.0127-0.5419-0.1418-0.43690.2161-0.34360.2630.73020.05740.03410.52780.09560.4438-30.37435.6817234.3074
552.6972-1.9077-0.92697.6064.37138.7106-0.08450.08210.2809-1.15780.1079-0.8652-0.41130.2939-0.00680.53670.04860.05010.61260.1040.5292-28.101739.2255233.5943
56-0.13730.09390.43122.70381.04236.02230.10390.30230.4403-0.486-0.1564-0.1391-0.3671-0.04640.06740.59260.0256-0.00520.6830.13860.6265-33.121745.8283237.0317
570.9269-1.4151.43812.74-0.56072.5693-0.08230.02120.1161-0.0003-0.0932-0.2783-0.09940.09840.15160.3945-0.06060.02850.57290.01840.5509-29.716239.4364253.9914
583.62921.7272-1.80843.12610.3662.41650.14450.15460.0412-0.0479-0.1792-0.1739-0.088-0.00610.02940.41270.0364-0.03880.49320.04940.4414-30.984233.7425250.9777
592.3905-1.2080.5292.3998-0.27411.4461-0.15460.0936-0.1366-0.1186-0.0202-0.33430.01820.2840.1370.5445-0.03880.120.60170.03680.6015-23.457323.3108246.5501
602.84351.51660.5384.9835-0.03830.90440.3358-0.5193-0.14020.2015-0.3139-0.35570.1812-0.08020.1410.817-0.0109-0.01840.69340.07390.5532-29.08355.9552286.4612
612.58971.17630.47715.82760.88424.0441-0.1587-0.4013-0.52050.7281-0.1443-0.55570.22080.41120.29690.749-0.02390.00670.68940.18010.6723-29.1976-2.6125286.0574
620.15760.661-0.52222.8664-0.56372.6382-0.0797-0.1501-0.20060.166-0.0799-0.370.23680.14360.09530.5040.00410.02140.62850.08070.5836-30.29541.9567269.7649
631.6426-1.55231.5193.18210.23072.40660.15640.2174-0.0389-0.0052-0.301-0.26460.03730.13210.12470.5734-0.08270.05490.58360.06940.4889-30.51237.9531269.8204
643.53181.8799-2.18822.786-1.17863.25770.0018-0.5197-0.43610.2018-0.2926-0.57610.11770.41160.30350.51840.0093-0.07840.65180.05670.5315-22.74518.4453273.9482
653.48350.0419-1.01354.78390.14692.52850.43850.16270.18890.4173-0.54940.27420.33350.51380.09440.6341-0.02640.08030.7101-0.06550.4357-35.364535.6061286.6793
662.64461.2580.01636.7528-4.50727.44140.0832-0.41290.37681.0215-0.21030.5286-0.2648-0.39930.16740.5824-0.06720.02540.7869-0.15880.5047-37.689239.1105287.4834
672.79340.6625-1.51695.5168-3.28168.7002-0.0365-0.65490.6140.44420.2180.18650.0153-0.6735-0.17260.62210.00230.00050.8474-0.1580.7028-37.742346.5469287.6647
682.8991-0.9122.51253.1106-1.11045.99310.1407-0.43270.48570.3212-0.1966-0.1996-0.1320.24750.06670.5514-0.0944-0.03560.6459-0.09910.5837-28.611444.9432281.2421
690.70751.71850.81912.69420.93073.1370.06440.08630.20680.1409-0.1670.234-0.0346-0.00950.07420.40880.0183-0.02390.6362-0.04680.5319-36.036639.3839267.1262
701.48930.5665-0.06742.4786-0.14191.92690.014-0.2843-0.04340.1266-0.1510.12490.0149-0.16230.12740.4824-0.01550.00010.5952-0.02970.4451-39.013827.7572272.4935
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'B' and (resid 20 through 44 )
3X-RAY DIFFRACTION3chain 'B' and (resid 45 through 96 )
4X-RAY DIFFRACTION4chain 'B' and (resid 97 through 109 )
5X-RAY DIFFRACTION5chain 'B' and (resid 110 through 156 )
6X-RAY DIFFRACTION6chain 'B' and (resid 157 through 202 )
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 258 )
8X-RAY DIFFRACTION8chain 'E' and (resid 2 through 44 )
9X-RAY DIFFRACTION9chain 'E' and (resid 45 through 96 )
10X-RAY DIFFRACTION10chain 'E' and (resid 97 through 156 )
11X-RAY DIFFRACTION11chain 'E' and (resid 157 through 243 )
12X-RAY DIFFRACTION12chain 'E' and (resid 244 through 258 )
13X-RAY DIFFRACTION13chain 'H' and (resid 2 through 41 )
14X-RAY DIFFRACTION14chain 'H' and (resid 42 through 54 )
15X-RAY DIFFRACTION15chain 'H' and (resid 55 through 96 )
16X-RAY DIFFRACTION16chain 'H' and (resid 97 through 156 )
17X-RAY DIFFRACTION17chain 'H' and (resid 157 through 202 )
18X-RAY DIFFRACTION18chain 'H' and (resid 203 through 258 )
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 19 )
20X-RAY DIFFRACTION20chain 'C' and (resid 20 through 67 )
21X-RAY DIFFRACTION21chain 'C' and (resid 68 through 96 )
22X-RAY DIFFRACTION22chain 'C' and (resid 97 through 134 )
23X-RAY DIFFRACTION23chain 'C' and (resid 135 through 178 )
24X-RAY DIFFRACTION24chain 'C' and (resid 179 through 258 )
25X-RAY DIFFRACTION25chain 'A' and (resid 2 through 19 )
26X-RAY DIFFRACTION26chain 'A' and (resid 20 through 67 )
27X-RAY DIFFRACTION27chain 'A' and (resid 68 through 109 )
28X-RAY DIFFRACTION28chain 'A' and (resid 110 through 134 )
29X-RAY DIFFRACTION29chain 'A' and (resid 135 through 156 )
30X-RAY DIFFRACTION30chain 'A' and (resid 157 through 258 )
31X-RAY DIFFRACTION31chain 'F' and (resid 2 through 19 )
32X-RAY DIFFRACTION32chain 'F' and (resid 20 through 44 )
33X-RAY DIFFRACTION33chain 'F' and (resid 45 through 96 )
34X-RAY DIFFRACTION34chain 'F' and (resid 97 through 156 )
35X-RAY DIFFRACTION35chain 'F' and (resid 157 through 178 )
36X-RAY DIFFRACTION36chain 'F' and (resid 179 through 258 )
37X-RAY DIFFRACTION37chain 'G' and (resid 2 through 19 )
38X-RAY DIFFRACTION38chain 'G' and (resid 20 through 96 )
39X-RAY DIFFRACTION39chain 'G' and (resid 97 through 109 )
40X-RAY DIFFRACTION40chain 'G' and (resid 110 through 177 )
41X-RAY DIFFRACTION41chain 'G' and (resid 178 through 258 )
42X-RAY DIFFRACTION42chain 'D' and (resid 2 through 19 )
43X-RAY DIFFRACTION43chain 'D' and (resid 20 through 67 )
44X-RAY DIFFRACTION44chain 'D' and (resid 68 through 96 )
45X-RAY DIFFRACTION45chain 'D' and (resid 97 through 109 )
46X-RAY DIFFRACTION46chain 'D' and (resid 110 through 156 )
47X-RAY DIFFRACTION47chain 'D' and (resid 157 through 180 )
48X-RAY DIFFRACTION48chain 'D' and (resid 181 through 258 )
49X-RAY DIFFRACTION49chain 'I' and (resid 2 through 19 )
50X-RAY DIFFRACTION50chain 'I' and (resid 20 through 80 )
51X-RAY DIFFRACTION51chain 'I' and (resid 81 through 156 )
52X-RAY DIFFRACTION52chain 'I' and (resid 157 through 202 )
53X-RAY DIFFRACTION53chain 'I' and (resid 203 through 258 )
54X-RAY DIFFRACTION54chain 'K' and (resid 2 through 19 )
55X-RAY DIFFRACTION55chain 'K' and (resid 20 through 44 )
56X-RAY DIFFRACTION56chain 'K' and (resid 45 through 96 )
57X-RAY DIFFRACTION57chain 'K' and (resid 97 through 156 )
58X-RAY DIFFRACTION58chain 'K' and (resid 157 through 202 )
59X-RAY DIFFRACTION59chain 'K' and (resid 203 through 258 )
60X-RAY DIFFRACTION60chain 'L' and (resid 2 through 19 )
61X-RAY DIFFRACTION61chain 'L' and (resid 20 through 80 )
62X-RAY DIFFRACTION62chain 'L' and (resid 81 through 156 )
63X-RAY DIFFRACTION63chain 'L' and (resid 157 through 202 )
64X-RAY DIFFRACTION64chain 'L' and (resid 203 through 258 )
65X-RAY DIFFRACTION65chain 'J' and (resid 2 through 19 )
66X-RAY DIFFRACTION66chain 'J' and (resid 20 through 44 )
67X-RAY DIFFRACTION67chain 'J' and (resid 45 through 67 )
68X-RAY DIFFRACTION68chain 'J' and (resid 68 through 96 )
69X-RAY DIFFRACTION69chain 'J' and (resid 97 through 156 )
70X-RAY DIFFRACTION70chain 'J' and (resid 157 through 258 )

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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