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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6sph | ||||||
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タイトル | A4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 WITH EBSELEN BOND IN C2 SPACE GROUP | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / A4V SOD1 mutant / MND / ALS | ||||||
機能・相同性 | ![]() action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Shahid, M. / Chantadul, V. / Amporndanai, K. / Wright, G. / Antonyuk, S. / Hasnain, S. | ||||||
![]() | ![]() タイトル: Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy. 著者: Chantadul, V. / Wright, G.S.A. / Amporndanai, K. / Shahid, M. / Antonyuk, S.V. / Washbourn, G. / Rogers, M. / Roberts, N. / Pye, M. / O'Neill, P.M. / Hasnain, S.S. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 198.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 157.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.3 MB | 表示 | |
XML形式データ | ![]() | 46.5 KB | 表示 | |
CIF形式データ | ![]() | 65.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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3 | ![]()
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単位格子 |
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Components on special symmetry positions |
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要素
-タンパク質 , 1種, 6分子 ACEGJL
#1: タンパク質 | 分子量: 15855.613 Da / 分子数: 6 / 変異: Ala4Val / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-非ポリマー , 6種, 830分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/9JT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9JT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-9JT / #4: 化合物 | ChemComp-GOL / #5: 化合物 | #6: 化合物 | ChemComp-DMS / #7: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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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: 4.3 Å3/Da / 溶媒含有率: 71.4 % |
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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: 100 mM Tris-HCl pH 7.4-8.0, 2.4-2.6 M ammonium sulphate, 150 mM NaCl PH範囲: 7.4-8.2 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() |
検出器 | タイプ: DECTRIS EIGER R 4M / 検出器: PIXEL / 日付: 2018年8月15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: 1.54179 Å / 相対比: 1 |
反射 | 解像度: 2.25→47.25 Å / Num. obs: 70706 / % possible obs: 97.3 % / 冗長度: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.3 |
反射 シェル | 解像度: 2.25→2.3 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4822 / CC1/2: 0.639 / % possible all: 97.7 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 1UXM 解像度: 2.25→43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / SU ML: 0.131 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.169 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 84.79 Å2 / Biso mean: 18.461 Å2 / Biso min: 8.75 Å2
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精密化ステップ | サイクル: final / 解像度: 2.25→43 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.25→2.308 Å
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