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- PDB-4zgs: Identification of the pyruvate reductase of Chlamydomonas reinhardtii -

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基本情報

登録情報
データベース: PDB / ID: 4zgs
タイトルIdentification of the pyruvate reductase of Chlamydomonas reinhardtii
要素Putative D-lactate dehydrogenase
キーワードOXIDOREDUCTASE / pyruvate dehydrogenase / fermentation / green alga / biohydrogen
機能・相同性
機能・相同性情報


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
類似検索 - 分子機能
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / 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 / Putative D-lactate dehydrogenase
類似検索 - 構成要素
生物種Chlamydomonas reinhardtii (クラミドモナス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.461 Å
データ登録者Burgess, S.J. / Hussein, T. / Yeoman, J.A. / Iamshanova, O. / Boehm, M. / Bundy, J. / Bialek, W. / Murray, J.W. / Nixon, P.J.
引用ジャーナル: Plant Cell.Physiol. / : 2016
タイトル: Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts.
著者: Burgess, S.J. / Taha, H. / Yeoman, J.A. / Iamshanova, O. / Chan, K.X. / Boehm, M. / Behrends, V. / Bundy, J.G. / Bialek, W. / Murray, J.W. / Nixon, P.J.
履歴
登録2015年4月23日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02015年12月2日Provider: repository / タイプ: Initial release
改定 1.12016年2月3日Group: Database references
改定 1.22018年4月11日Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
改定 1.32018年9月19日Group: Data collection / カテゴリ: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
改定 1.42024年1月10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: Putative D-lactate dehydrogenase
B: Putative D-lactate dehydrogenase
C: Putative D-lactate dehydrogenase
D: Putative D-lactate dehydrogenase
E: Putative D-lactate dehydrogenase
F: Putative D-lactate dehydrogenase
G: Putative D-lactate dehydrogenase
H: Putative D-lactate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)341,95816
ポリマ-336,6508
非ポリマー5,3078
3,927218
1
A: Putative D-lactate dehydrogenase
B: Putative D-lactate dehydrogenase
C: Putative D-lactate dehydrogenase
D: Putative D-lactate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)170,9798
ポリマ-168,3254
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-104 kcal/mol
Surface area49400 Å2
手法PISA
2
E: Putative D-lactate dehydrogenase
F: Putative D-lactate dehydrogenase
G: Putative D-lactate dehydrogenase
H: Putative D-lactate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)170,9798
ポリマ-168,3254
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-105 kcal/mol
Surface area49550 Å2
手法PISA
単位格子
Length a, b, c (Å)83.760, 110.920, 193.160
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Putative D-lactate dehydrogenase / Pyruvate reductase


分子量: 42081.312 Da / 分子数: 8 / 断片: UNP residues 45-421 / 由来タイプ: 組換発現
由来: (組換発現) Chlamydomonas reinhardtii (クラミドモナス)
遺伝子: Cre07.g324550 / Organelle: chloroplast / プラスミド: pET28b / 発現宿主: Escherichia coli KRX (大腸菌) / 参照: UniProt: B0LUZ5
#2: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 8 / 由来タイプ: 組換発現 / : C21H27N7O14P2 / 参照: D-lactate dehydrogenase / コメント: NAD*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 218 / 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

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試料調製

結晶マシュー密度: 2.63 Å3/Da / 溶媒含有率: 53.23 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: 1:1 10mg/ml protein with 0.2M sodium malonate pH 6.0 20% w/v PEG 3350

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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: Diamond / ビームライン: I02 / 波長: 0.9795 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2012年10月1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: 0.9795 Å / 相対比: 1
反射解像度: 2.46→66.84 Å / Num. all: 126464 / Num. obs: 126464 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2.6 % / Rmerge(I) obs: 0.071 / Net I/av σ(I): 8.4 / Net I/σ(I): 8.6
反射 シェル解像度: 2.46→2.52 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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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
xia2データ削減
xia2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: 2DLD
解像度: 2.461→66.84 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.76 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2541 6334 5.01 %
Rwork0.2023 --
obs0.205 126315 98.52 %
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: 2.461→66.84 Å
タンパク質核酸リガンド溶媒全体
原子数21433 0 44 218 21695
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.01121900
X-RAY DIFFRACTIONf_angle_d1.52129793
X-RAY DIFFRACTIONf_dihedral_angle_d12.4457920
X-RAY DIFFRACTIONf_chiral_restr0.0683499
X-RAY DIFFRACTIONf_plane_restr0.0083779
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4608-2.48880.39672060.35333971X-RAY DIFFRACTION99
2.4888-2.51810.41172160.31684008X-RAY DIFFRACTION99
2.5181-2.54880.35161930.29084010X-RAY DIFFRACTION99
2.5488-2.5810.34641970.28594046X-RAY DIFFRACTION99
2.581-2.6150.36132100.27673966X-RAY DIFFRACTION98
2.615-2.65080.32871980.28133966X-RAY DIFFRACTION98
2.6508-2.68870.37952110.28273998X-RAY DIFFRACTION99
2.6887-2.72880.34152170.26413987X-RAY DIFFRACTION99
2.7288-2.77150.32132140.25614021X-RAY DIFFRACTION99
2.7715-2.81690.30142080.24973963X-RAY DIFFRACTION99
2.8169-2.86550.29582010.22514024X-RAY DIFFRACTION99
2.8655-2.91760.2782390.22873985X-RAY DIFFRACTION99
2.9176-2.97370.32812250.244024X-RAY DIFFRACTION99
2.9737-3.03440.30192090.24623942X-RAY DIFFRACTION99
3.0344-3.10040.28772000.24194078X-RAY DIFFRACTION99
3.1004-3.17250.31982020.26273992X-RAY DIFFRACTION99
3.1725-3.25180.30662510.25223972X-RAY DIFFRACTION98
3.2518-3.33970.32132030.22853983X-RAY DIFFRACTION99
3.3397-3.4380.27491970.21964022X-RAY DIFFRACTION99
3.438-3.5490.28642150.20383986X-RAY DIFFRACTION98
3.549-3.67580.20672030.17774016X-RAY DIFFRACTION99
3.6758-3.8230.2172270.17724041X-RAY DIFFRACTION99
3.823-3.99690.2052270.16653969X-RAY DIFFRACTION99
3.9969-4.20760.20462320.1624001X-RAY DIFFRACTION99
4.2076-4.47120.20321940.15734045X-RAY DIFFRACTION99
4.4712-4.81630.19221940.14523982X-RAY DIFFRACTION98
4.8163-5.30090.19742150.16644000X-RAY DIFFRACTION98
5.3009-6.06750.25052060.18524011X-RAY DIFFRACTION98
6.0675-7.64260.2552220.18854012X-RAY DIFFRACTION97
7.6426-66.86730.18942020.15993960X-RAY DIFFRACTION94
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)
10.05740.05390.04460.0789-0.01230.12970.57460.0266-0.2519-0.17210.27440.17480.077-0.0769-0.64191.4062-0.1168-0.11912.022-0.43942.629338.793915.370549.4961
20.0052-0.01830.00690.1487-0.05570.02230.2678-0.1458-0.38080.15-0.19860.0260.1898-0.3557-0.03381.5761-0.0096-0.18382.7738-0.36812.209142.9636-15.611921.3915
30.0507-0.01170.00650.00470.00040.00310.45660.18090.08820.3399-0.1795-0.4754-0.29480.1409-0.31961.93720.04140.37843.1112-0.35142.9003-14.49658.29221.2149
40.18520.81830.08123.80870.31870.28630.03470.0277-0.11630.3073-0.0126-0.0697-0.03630.4128-0.06351.0094-0.0556-0.3422.5268-0.52662.4844-10.3612-22.241349.531
50.0114-0.01250.01140.0121-0.00970.02090.2105-0.2562-0.2374-0.26520.15570.5649-0.0216-0.6366-0.18211.1495-0.49810.12472.4511-0.74242.421351.775370.242874.9695
60.01950.0055-0.00810.11840.11520.11980.7653-0.0577-0.12910.1212-0.06380.0556-0.0654-0.2326-0.41130.8043-0.21120.16853.0966-0.04522.723756.318138.879147.3389
73.8788-2.8403-0.00073.8902-1.27020.8911.11050.0550.34660.57950.0866-0.55220.31690.6356-0.74240.6978-0.0661-0.36622.04880.09281.7586-1.400561.987846.9514
81.33992.80441.11245.87012.33260.9215-0.0937-0.1010.01740.0699-0.170.28470.04760.11910.12171.4457-0.29510.02552.4720.17772.20722.745331.819475.7089
92.95920.20322.07672.77430.39036.97540.0244-0.6901-0.36430.58870.1702-0.43570.21740.0876-0.09610.44570.022-0.0760.79360.03220.372730.6681-4.615869.688
108.43271.7522-2.10587.44882.09281.9211-0.0388-0.84690.34070.246-0.16320.4524-0.0581-0.59590.16970.49630.04320.02350.85650.0090.428520.3863.616769.1739
116.4811-3.3159-2.68254.53420.57253.44770.32040.04911.12520.9303-0.57540.71830.0331-1.12850.39360.65110.0140.0751.1107-0.3720.713122.968311.548473.5837
127.1593-2.1138-0.47292.0641-3.03828.453-0.3001-0.42252.61690.1932-0.60190.8006-0.63-0.49730.78050.6798-0.0153-0.08980.6882-0.25991.179627.391715.676767.4179
135.2423-0.8119-3.28774.2583-0.95179.1185-0.8355-0.11250.43720.0968-0.1715-0.0322-0.3857-0.92960.83910.5969-0.0252-0.08320.5878-0.15620.486335.12099.83464.5481
145.31331.68220.62712.52751.3383.14160.25880.29030.4496-0.0696-0.02390.0356-0.11450.1927-0.19270.27210.06370.06250.30240.00420.298534.82613.136533.3287
153.53870.1945-0.59081.98620.0981.58720.3175-0.19291.54660.06480.0808-0.1459-0.3310.2203-0.26570.412-0.05890.15410.356-0.13020.781935.077318.798437.1463
163.8051-0.1407-0.4133.2735-2.86772.94320.2064-0.33010.64060.2410.00410.0265-0.24640.2347-0.19990.35730.04660.05010.5721-0.19210.383313.474910.457645.8471
173.8319-2.09654.95533.4198-3.48818.5420.3734-0.90930.13260.2068-0.21840.02170.04870.1034-0.21290.28080.02950.07960.49350.00160.391929.52972.495646.1364
180.54981.38490.96474.6089-0.00156.5203-0.0241-1.03610.70020.6620.0867-0.5569-0.08530.8382-0.04880.5001-0.0563-0.06761.0414-0.23430.395738.60615.722170.0822
191.25850.77360.17171.78811.58691.69020.1317-0.3082-0.01210.4278-0.29080.21330.3709-0.4821-0.20811.87850.3577-0.04261.9669-0.1701-0.237632.6039-0.7475-6.1414
202.1532-2.1293-0.29182.5915-1.06583.6268-0.41451.4279-0.1663-1.25970.10760.3283-0.1669-1.71950.38131.1207-0.082-0.05341.7776-0.11590.490324.5143-2.46624.5173
210.91950.3861.54440.62721.03512.8141-0.26740.5813-0.8131-0.0768-0.45520.52071.2568-1.85460.29441.6226-0.7736-0.04892.4451-0.505-0.218225.9726-13.2768-0.3622
226.1642-0.1470.48660.73180.05890.0419-1.34280.3416-1.11860.5722-1.45490.55991.3182-1.39912.31722.0972-0.54840.20391.5387-0.3390.79332.6556-20.26663.23
233.0248-1.20480.29812.7412-0.22783.016-0.30610.391-0.7243-0.58790.2196-0.25030.8745-0.108-0.07121.57650.14340.14761.1365-0.7420.660738.148-11.55456.5596
246.7723-1.2941-3.43441.42231.99425.25660.3937-0.0466-0.1554-0.0709-0.20540.0481-0.0883-0.2008-0.14270.271-0.0041-0.02030.2573-0.00740.26528.5176-2.334838.8061
252.6791.68951.84324.5211-1.26743.39750.25930.2118-0.6191-0.1176-0.1226-0.24250.13850.2353-0.17130.20650.0591-0.04110.4938-0.07640.453647.2478-9.755233.7017
264.53720.7553-1.02511.1647-0.49831.85350.0030.3061-0.9446-0.02120.0105-0.36180.28990.24970.04470.30050.0807-0.03360.3991-0.11170.551339.4306-19.621833.7914
273.05642.43810.29862.6307-0.78441.49390.00141.1994-0.5158-0.28940.1782-0.12590.1679-0.3817-0.12180.3680.05980.05620.7734-0.20360.485319.5292-15.536525.7216
281.0961-0.1875-2.38591.29910.9685.53540.31240.93610.1924-0.44750.6068-0.6487-0.03380.985-0.68020.5870.1180.07041.5466-0.18380.415439.2465-3.33955.0573
290.50850.3727-0.19261.2179-0.36350.1259-0.2050.85180.1707-0.2901-0.0928-0.89781.6437-0.4270.30210.9156-0.0759-0.08811.27550.00590.560457.511249.1935103.1556
300.80611.4306-0.54833.63670.9883.88420.2527-1.30280.47160.7627-0.3190.2536-0.424-1.40450.08090.71520.0304-0.02681.6218-0.15730.509937.957454.140995.0479
312.4512-0.0367-2.23450.00730.08792.5280.342-0.31461.60040.6111.1183-0.3614-0.04220.7008-1.15841.19890.3766-0.14271.5199-0.70291.342633.76668.516191.2194
321.5307-0.2735-1.42453.7328-2.38453.19980.2451-0.57840.8590.3418-0.87820.2110.3552-0.33580.27950.9140.03180.07781.4844-0.45130.608339.306264.702496.717
335.19150.36460.11154.2087-0.94626.76061.08330.11041.1238-1.2517-0.21041.3069-1.1259-0.1396-0.65231.78180.3878-0.19151.1149-0.38791.130139.645273.604795.2608
345.41290.8892-1.69485.0972-2.64221.6651-0.4817-0.77541.0190.52-0.26590.0495-1.3096-1.6560.54890.92380.118-0.20831.0651-0.26360.639248.320464.790590.1364
355.06972.13551.85643.27993.1335.51340.14440.06930.39290.0654-0.07110.08150.0303-0.0783-0.11670.26980.05070.02150.3833-0.0120.335441.777253.572457.5079
362.9559-0.32280.62392.1351-0.4961.8250.0226-0.52681.2636-0.01650.087-0.1631-0.2270.2005-0.06570.3217-0.0390.06770.4199-0.18860.724150.319370.914562.5284
375.8085-2.4113-1.09832.2724-0.55080.93710.0192-0.99680.85460.22120.089-0.0535-0.1242-0.11-0.13920.3444-0.00290.00470.5867-0.20910.516929.231463.937270.614
380.6656-0.56341.54211.27760.26247.40310.3875-0.65630.29850.5023-0.0451-0.6826-0.92710.8827-0.24160.7667-0.2747-0.06551.3068-0.20950.47851.400957.384391.8021
392.56133.5396-1.68579.0155-4.89272.70230.2224-0.04750.5421-0.2293-0.2647-0.6548-2.11621.53880.15511.7928-0.62370.04681.30910.2550.374354.598459.47617.4333
401.2046-0.6213-2.69191.17531.89316.3046-0.0291.18610.6104-1.0933-0.18110.1937-0.2571-0.28620.18460.7930.0428-0.04231.3110.11070.436439.187653.729229.1442
412.3554-0.73441.43640.39040.00992.09650.44740.7037-0.8477-0.1612-0.28760.41121.5575-1.128-0.0281.3301-0.4693-0.05361.5484-0.15290.582538.164940.674624.8804
425.65140.6606-0.69821.58611.41051.5594-0.84320.8188-1.4598-0.62950.0354-0.48131.4370.02640.56771.74840.06570.1140.8791-0.19060.608647.402237.45429.0347
436.8577-0.8789-2.47792.41521.66074.95830.2794-0.0685-0.1179-0.0108-0.17930.1579-0.2092-0.2978-0.09210.2352-0.0052-0.02850.3844-0.03280.301642.260351.780763.3746
443.69751.70612.01244.678-1.37015.2061-0.0516-0.0994-0.35590.239-0.1205-0.46550.07020.4680.07670.2259-0.0178-0.02690.4858-0.05430.3960.366344.615959.6985
454.67490.7833-0.63341.6108-0.62251.2431-0.17830.0649-1.26110.01450.1105-0.37410.28120.20750.04780.30220.05820.00350.3643-0.10720.563652.182934.683259.6194
461.63382.6956-1.3524.9915-2.66834.7332-0.13030.7925-0.6395-0.49830.1747-0.33380.1210.45490.01450.4018-0.0153-0.00870.7853-0.22350.67228.739237.356148.304
471.52761.1502-1.02112.7916-1.88114.9714-0.20470.8383-0.1018-0.24840.2008-0.20430.0146-0.01340.19060.27330.0634-0.02870.7552-0.09510.383845.61534842.7993
482.8972-0.3663-2.86191.06461.39153.8787-0.20440.0743-0.17540.11260.13070.07640.41950.18540.33991.32990.77470.17811.7479-0.4820.719157.381544.226226.2404
490.1921-0.57810.37461.7619-1.19120.80910.0769-0.0872-0.22910.04250.17690.39881.80470.73610.04422.1201-0.31140.28361.6384-0.10150.3482-7.0335-9.6351-7.4606
500.7103-1.06890.65812.67550.27652.1190.01012.533-0.3028-1.43250.0765-0.48630.42631.0013-0.02340.98410.11480.0291.979-0.0970.65882.9157-7.76844.9808
517.409-1.95771.17161.15240.86742.38040.3221-0.02391.1665-0.0093-0.0475-0.4973-1.29311.0546-0.26041.5309-1.413-0.07812.5237-0.13240.74749.8735.905-0.8735
521.505-0.4796-0.67472.24280.74887.45410.0648-0.0410.32350.4668-0.34380.1181-0.30430.5115-0.21641.2827-0.66970.03182.68030.06750.19782.05681.41271.2663
530.7068-0.99950.26021.4119-0.36780.09170.70710.30470.7277-1.40870.153-1.403-0.17030.1389-0.38241.946-1.02670.33522.00730.15321.2611.97079.0572-3.3489
545.15321.18930.51691.36921.07641.6374-1.4510.32891.4248-0.46750.58820.1414-1.59350.53810.89181.5446-0.1057-0.15581.60030.2430.7578-6.13178.00594.2099
553.1060.74310.55860.7567-0.25991.03440.10660.26120.4479-0.02240.01040.1625-0.1161-0.0286-0.09670.30340.04710.05880.5080.00370.3835-9.69385.963234.8052
563.27533.14733.17823.38664.01148.7616-0.37621.35060.704-0.2160.45010.1788-0.17990.2009-0.26920.45670.01960.04220.92150.10370.630412.659.746121.7498
572.75791.38922.18523.00843.25267.0721-0.08450.83970.0477-0.1809-0.02920.1980.16410.32920.10050.32350.11130.05990.7548-0.00740.3626-1.1836-0.005823.217
583.4461-0.9214-0.34182.8473-2.52769.80970.0267-0.4649-0.40260.14260.87910.5609-1.2232-0.6883-0.34870.85330.1067-0.27022.07720.25020.5107-13.5204-1.1343-2.226
595.70246.11071.99576.70192.20050.8414-0.25641.2743-0.6167-0.64610.5476-0.4046-0.26070.81-0.29171.2564-0.08870.25671.8096-0.07161.3704-17.7617-1.358175.2291
600.50680.4784-1.80531.4871-0.74287.60220.402-1.724-0.0610.6507-0.2744-0.0289-0.56271.3083-0.10920.648-0.11640.06441.216-0.03320.44221.55-3.091468.2673
616.84450.90461.74524.5204-0.16644.42630.4828-1.4107-1.76680.325-0.4133-0.79130.04130.61670.16680.6730.0926-0.04771.25310.25050.78925.3256-16.994869.7113
627.94951.4713-0.07144.82671.2713.1415-0.441-1.3973-0.98780.72970.037-0.68930.34490.68770.2530.9445-0.1398-0.08941.17520.24320.5284-4.3733-18.647767.6246
634.13311.8495-1.55152.6988-1.05982.53580.11030.5227-0.4153-0.2401-0.0454-0.12070.04420.0959-0.07840.24320.0589-0.04830.4125-0.07320.33-6.1496-9.94833.4765
644.2957-1.0992-0.5343.6249-0.41263.27020.07560.3443-1.11180.0132-0.07170.2320.3214-0.1477-0.07550.338-0.0327-0.07510.5218-0.01850.6306-11.8893-27.014839.2823
653.532-1.132-1.25044.00781.0546.08340.00250.3314-0.6928-0.17540.11860.10350.1932-0.1831-0.16830.24920.0197-0.01670.4266-0.09970.58170.9529-23.648735.593
665.33724.32662.53763.70040.97697.4055-0.1218-0.3994-1.66160.5199-0.03350.7627-0.2646-0.67570.06170.66940.15-0.19080.87990.14421.00918.5299-21.424249.5676
676.0237-0.26441.68361.85520.63860.71420.0936-0.794-0.58530.10030.0526-0.1988-0.04640.0279-0.1530.3026-0.0243-0.0290.475-0.01620.347312.9223-15.407344.5304
683.7601-0.5235-3.11234.11980.125.5550.2878-0.7033-0.14490.77950.14160.87420.1634-1.128-0.43430.4717-0.15090.06820.95060.01980.422-9.686-9.231166.0116
690.6729-0.9572-0.80591.53250.23794.4381-0.3361.4719-0.1599-1.27680.3401-0.3680.10271.88310.16131.1232-0.1029-0.0591.3675-0.09220.477113.031845.642726.9612
701.6618-0.0206-0.6930.50.00990.27710.31861.02790.96030.2388-0.42-0.3953-1.26831.01560.41521.5914-0.775-0.16121.92930.26710.627317.409960.417125.5848
713.5898-0.79752.2520.1708-0.49791.4168-1.25940.56351.51850.119-0.2804-0.2985-3.04640.31421.03752.5941-0.254-0.56471.40310.23080.80038.262463.690228.9935
722.4801-0.9230.5521.33671.11581.8522-0.4469-0.2550.6247-0.35650.16990.2708-1.8306-0.09330.1941.80710.4153-0.5461.42890.23150.76693.105157.353932.1812
735.9354-1.46832.89461.0629-1.82723.92970.1341-0.73970.24650.1013-0.1011-0.17320.0568-0.0364-0.02880.2452-0.0335-0.01470.3789-0.03110.239913.032849.558264.7687
743.65030.6795-0.36482.84270.472.1903-0.0172-0.38910.82460.0666-0.00410.3498-0.0313-0.46340.02860.20420.05270.03330.4018-0.05640.5248-6.03160.159758.3939
753.519-0.52131.65554.51621.74934.9626-0.23260.01411.16520.0020.20920.016-0.58750.10960.02280.2575-0.01250.0130.2855-0.08750.71438.385568.475459.6226
760.4050.76520.46896.1013.065.10180.31260.37660.1011-0.28840.0407-0.36660.0126-0.1471-0.35430.3505-0.0209-0.02890.62870.08670.518126.354963.38647.8182
776.44043.59844.48845.55594.77398.2641-0.0370.73730.38920.06340.0820.0930.17420.3176-0.1660.25550.0780.03290.38320.00490.389612.721454.41551.2963
784.1255-1.30162.90791.558-0.39692.2638-0.76670.87420.4381-0.87710.44040.8083-1.1295-1.92610.17570.96320.074-0.3031.4586-0.08910.38470.138252.149125.4034
790.43831.1071-0.90322.9903-1.2116.48390.4146-1.5284-0.03960.60980.05610.1843-0.00480.944-0.33380.5765-0.06360.05321.3223-0.08930.435412.884151.868395.0823
805.80680.02141.56864.6176-1.40841.247-0.0317-1.0965-1.22880.4253-0.1298-0.49530.68561.4342-0.0260.84110.0891-0.03611.7060.15290.584321.417639.490297.1627
814.49250.60313.90222.17890.21693.444-0.2677-0.8827-0.4066-0.5332-0.50080.0970.59550.62550.64540.74140.07490.03221.0820.16150.503112.784437.800692.386
822.54910.99681.54982.66764.52717.69981.0699-1.0011-1.5373-1.3009-0.7914-0.78581.31530.2599-0.30791.49070.48570.10651.30220.32561.071214.735529.565399.3499
833.2106-0.28392.1722.8438-0.67487.34520.0806-0.2524-0.48340.2340.28040.311.5052-0.0438-0.35610.9176-0.01110.12081.04120.21490.66885.662838.380589.7248
847.36713.0293-3.47333.0146-3.5554.58090.2946-0.1527-0.353-0.0066-0.2491-0.1337-0.0799-0.0521-0.02060.26950.0385-0.02790.2315-0.07590.266513.243347.87957.7578
854.0212-0.68090.75385.05231.87873.17180.1264-0.5786-0.6739-0.0237-0.0880.42660.2628-0.096-0.03540.2865-0.0377-0.08330.57130.05530.5134-2.811135.980363.149
865.0722-0.4055-0.33752.1570.20642-0.0074-0.4576-1.42230.06280.11060.09840.4033-0.0421-0.11720.3292-0.0337-0.08340.37280.10350.64257.340528.510263.3458
877.4904-1.9722-0.52952.76380.56890.1442-0.1357-1.308-0.48570.32430.1237-0.01690.01240.44050.03770.35490.00670.00970.50570.07710.338525.10138.238771.2558
883.1743-0.3691-1.79093.02091.71142.16090.4816-1.1684-0.22481.06540.13660.4377-0.0859-1.0503-0.54070.6052-0.16320.03481.24430.03390.50593.038145.389692.5712
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1000:1000)
2X-RAY DIFFRACTION2(chain B and resid 1000:1000)
3X-RAY DIFFRACTION3(chain C and resid 1000:1000)
4X-RAY DIFFRACTION4(chain D and resid 1000:1000)
5X-RAY DIFFRACTION5(chain E and resid 1000:1000)
6X-RAY DIFFRACTION6(chain F and resid 1000:1000)
7X-RAY DIFFRACTION7(chain G and resid 1000:1000)
8X-RAY DIFFRACTION8(chain H and resid 1000:1000)
9X-RAY DIFFRACTION9(chain A and resid 25:59)
10X-RAY DIFFRACTION10(chain A and resid 60:89)
11X-RAY DIFFRACTION11(chain A and resid 90:108)
12X-RAY DIFFRACTION12(chain A and resid 109:125)
13X-RAY DIFFRACTION13(chain A and resid 126:134)
14X-RAY DIFFRACTION14(chain A and resid 135:205)
15X-RAY DIFFRACTION15(chain A and resid 206:293)
16X-RAY DIFFRACTION16(chain A and resid 294:327)
17X-RAY DIFFRACTION17(chain A and resid 328:345)
18X-RAY DIFFRACTION18(chain A and resid 346:370)
19X-RAY DIFFRACTION19(chain B and resid 29:39)
20X-RAY DIFFRACTION20(chain B and resid 40:72)
21X-RAY DIFFRACTION21(chain B and resid 73:109)
22X-RAY DIFFRACTION22(chain B and resid 110:125)
23X-RAY DIFFRACTION23(chain B and resid 126:134)
24X-RAY DIFFRACTION24(chain B and resid 135:175)
25X-RAY DIFFRACTION25(chain B and resid 176:210)
26X-RAY DIFFRACTION26(chain B and resid 211:293)
27X-RAY DIFFRACTION27(chain B and resid 294:338)
28X-RAY DIFFRACTION28(chain B and resid 339:366)
29X-RAY DIFFRACTION29(chain E and resid 24:29)
30X-RAY DIFFRACTION30(chain E and resid 30:85)
31X-RAY DIFFRACTION31(chain E and resid 86:95)
32X-RAY DIFFRACTION32(chain E and resid 96:113)
33X-RAY DIFFRACTION33(chain E and resid 114:125)
34X-RAY DIFFRACTION34(chain E and resid 126:134)
35X-RAY DIFFRACTION35(chain E and resid 135:176)
36X-RAY DIFFRACTION36(chain E and resid 177:293)
37X-RAY DIFFRACTION37(chain E and resid 294:338)
38X-RAY DIFFRACTION38(chain E and resid 339:367)
39X-RAY DIFFRACTION39(chain F and resid 26:32)
40X-RAY DIFFRACTION40(chain F and resid 33:68)
41X-RAY DIFFRACTION41(chain F and resid 69:108)
42X-RAY DIFFRACTION42(chain F and resid 109:132)
43X-RAY DIFFRACTION43(chain F and resid 133:175)
44X-RAY DIFFRACTION44(chain F and resid 176:210)
45X-RAY DIFFRACTION45(chain F and resid 211:295)
46X-RAY DIFFRACTION46(chain F and resid 296:321)
47X-RAY DIFFRACTION47(chain F and resid 322:361)
48X-RAY DIFFRACTION48(chain F and resid 362:368)
49X-RAY DIFFRACTION49(chain C and resid 26:38)
50X-RAY DIFFRACTION50(chain C and resid 39:67)
51X-RAY DIFFRACTION51(chain C and resid 68:76)
52X-RAY DIFFRACTION52(chain C and resid 77:88)
53X-RAY DIFFRACTION53(chain C and resid 89:106)
54X-RAY DIFFRACTION54(chain C and resid 107:134)
55X-RAY DIFFRACTION55(chain C and resid 135:294)
56X-RAY DIFFRACTION56(chain C and resid 295:320)
57X-RAY DIFFRACTION57(chain C and resid 321:352)
58X-RAY DIFFRACTION58(chain C and resid 353:367)
59X-RAY DIFFRACTION59(chain D and resid 22:28)
60X-RAY DIFFRACTION60(chain D and resid 29:68)
61X-RAY DIFFRACTION61(chain D and resid 69:122)
62X-RAY DIFFRACTION62(chain D and resid 123:134)
63X-RAY DIFFRACTION63(chain D and resid 135:204)
64X-RAY DIFFRACTION64(chain D and resid 205:255)
65X-RAY DIFFRACTION65(chain D and resid 256:294)
66X-RAY DIFFRACTION66(chain D and resid 295:300)
67X-RAY DIFFRACTION67(chain D and resid 301:338)
68X-RAY DIFFRACTION68(chain D and resid 339:367)
69X-RAY DIFFRACTION69(chain G and resid 26:65)
70X-RAY DIFFRACTION70(chain G and resid 66:104)
71X-RAY DIFFRACTION71(chain G and resid 105:125)
72X-RAY DIFFRACTION72(chain G and resid 126:134)
73X-RAY DIFFRACTION73(chain G and resid 135:175)
74X-RAY DIFFRACTION74(chain G and resid 176:244)
75X-RAY DIFFRACTION75(chain G and resid 245:296)
76X-RAY DIFFRACTION76(chain G and resid 297:321)
77X-RAY DIFFRACTION77(chain G and resid 322:348)
78X-RAY DIFFRACTION78(chain G and resid 349:368)
79X-RAY DIFFRACTION79(chain H and resid 25:68)
80X-RAY DIFFRACTION80(chain H and resid 69:101)
81X-RAY DIFFRACTION81(chain H and resid 102:115)
82X-RAY DIFFRACTION82(chain H and resid 116:126)
83X-RAY DIFFRACTION83(chain H and resid 127:134)
84X-RAY DIFFRACTION84(chain H and resid 135:175)
85X-RAY DIFFRACTION85(chain H and resid 176:210)
86X-RAY DIFFRACTION86(chain H and resid 211:293)
87X-RAY DIFFRACTION87(chain H and resid 294:339)
88X-RAY DIFFRACTION88(chain H and resid 340:367)

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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

-
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。

-
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