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基本情報
登録情報 | データベース: PDB / ID: 2vl9 | ||||||
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タイトル | Oxidized form of human peroxiredoxin 5 | ||||||
![]() | PEROXIREDOXIN-5 | ||||||
![]() | OXIDOREDUCTASE / THIOREDOXIN PEROXIDASE / ALTERNATIVE INITIATION / ANTIOXIDANT ENZYME / REDOX-ACTIVE CENTER / CYTOPLASM / PEROXIDASE / PEROXISOME / ANTIOXIDANT / POLYMORPHISM / MITOCHONDRION / PEROXIREDOXIN / TRANSIT PEPTIDE / THIOREDOXIN FOLD | ||||||
機能・相同性 | ![]() peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species / antioxidant activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to reactive oxygen species / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Smeets, A. / Declercq, J.P. | ||||||
![]() | ![]() タイトル: The Crystal Structures of Oxidized Forms of Human Peroxiredoxin 5 with an Intramolecular Disulfide Bond Confirm the Proposed Enzymatic Mechanism for Atypical 2-Cys Peroxiredoxins. 著者: Smeets, A. / Marchand, C. / Linard, D. / Knoops, B. / Declercq, J.P. | ||||||
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 | ![]() | 129.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 101.6 KB | 表示 | ![]() |
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その他 | ![]() |
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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: 18308.979 Da / 分子数: 4 / 断片: RESIDUES 2-162 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 水 | ChemComp-HOH / | 構成要素の詳細 | ENGINEERED RESIDUE IN CHAIN A, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 73 TO SER ...ENGINEERED | |
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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: 2.22 Å3/Da / 溶媒含有率: 44.53 % 解説: THE MODEL USED FOR THE MOLECULAR REPLACEMENT WAS A SIMULATION CREATED FROM PDB ENTRY 1OC3 |
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結晶化 | pH: 6.5 詳細: PEG 8000 20% SODIUM CACODYLATE 0.1 M PH 6.5 SODIUM ACETATE 0.1 M 6-AMINOCAPROIC ACID 3% W/V |
-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: MARRESEARCH / 検出器: CCD / 日付: 2005年11月11日 / 詳細: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING |
放射 | モノクロメーター: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT 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: 0.979764 Å / 相対比: 1 |
Reflection twin | Operator: -K,H+K,L / Fraction: 0.479 |
反射 | 解像度: 2.7→46 Å / Num. obs: 18076 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / 冗長度: 4.05 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9 |
反射 シェル | 解像度: 2.7→2.75 Å / 冗長度: 4.05 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6 |
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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 1OC3 解像度: 2.7→46 Å / 位相誤差: 24.5 / 立体化学のターゲット値: TWIN_LSQ_F 詳細: TWIN RATIO IS 50%. COMPUTED STRUCTURE FACTORS ARE NOT DIRECTLY COMPARABLE TO THE DEPOSITED OBSERVED STRUCTURE FACTORS.
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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 / Bsol: 170.46 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 79.53 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.7→46 Å
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拘束条件 |
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