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基本情報
登録情報 | データベース: PDB / ID: 2or3 | ||||||
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タイトル | Pre-oxidation Complex of Human DJ-1 | ||||||
![]() | Protein DJ-1 | ||||||
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機能・相同性 | ![]() tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glycolate biosynthetic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of autophagy of mitochondrion / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Witt, A.C. / Lakshminarasimhan, M. / Wilson, M.A. | ||||||
![]() | ![]() タイトル: Cysteine pKa depression by a protonated glutamic acid in human DJ-1. 著者: Witt, A.C. / Lakshminarasimhan, M. / Remington, B.C. / Hasim, S. / Pozharski, E. / Wilson, M.A. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 181.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 144.4 KB | 表示 | ![]() |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 19917.051 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() ![]() #2: 化合物 | ![]() #3: 水 | ChemComp-HOH / | ![]() |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.33 Å3/Da / 溶媒含有率: 47.32 % |
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結晶化![]() | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 詳細: 28% PEG 4000, 200 mM ammonium sulfate, 50 mM sodium acetate, 2.5 mM epigallocatechin 3-gallate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2006年3月12日 / 詳細: BENT CONICAL Si MIRROR |
放射 | モノクロメーター: BENT Ge(111) / 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![]() |
反射 | 解像度: 1.2→22.45 Å / Num. all: 114729 / Num. obs: 114729 / % possible obs: 97.8 % / 冗長度: 5.3 % / Biso Wilson estimate: 8.9 Å2 / Rsym value: 0.065 / Net I/σ(I): 24.3 |
反射 シェル | 解像度: 1.2→1.24 Å / 冗長度: 4.2 % / Mean I/σ(I) obs: 2.04 / Num. unique all: 11105 / Rsym value: 0.702 / % possible all: 96 |
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解析
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精密化 | 構造決定の手法![]() ![]() 開始モデル: pdb entry 1P5F 解像度: 1.2→22.45 Å / Num. parameters: 31968 / Num. restraintsaints: 40468 / 交差検証法: FREE R / σ(F): 0 / 立体化学のターゲット値: ENGH & HUBER 詳細: Authors state that there were slight model changes after combining the test and working set, so the final R factor is lower than the working R factor.
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Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 2794 / Occupancy sum non hydrogen: 3302.5 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.2→22.45 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.2→1.24 Å /
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