+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7klb | |||||||||
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タイトル | X-ray Counterpart to Neutron Structure of Reduced Human MnSOD | |||||||||
要素 | Superoxide dismutase [Mn], mitochondrial | |||||||||
キーワード | OXIDOREDUCTASE / Antioxidant / SOD / Superoxide | |||||||||
機能・相同性 | 機能・相同性情報 acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / response to zinc ion / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / response to axon injury / response to hyperoxia / neuron development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / respiratory electron transport chain / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / liver development / regulation of mitochondrial membrane potential / response to activity / locomotory behavior / response to gamma radiation / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / multicellular organismal-level iron ion homeostasis / oxygen binding / regulation of blood pressure / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / 分子置換 / 解像度: 2.16 Å | |||||||||
データ登録者 | Azadmanesh, J. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Borgstahl, G.E.O. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. 著者: Azadmanesh, J. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Borgstahl, G.E.O. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7klb.cif.gz | 182.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7klb.ent.gz | 138.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7klb.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kl/7klb ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7klb | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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Components on special symmetry positions |
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非結晶学的対称性 (NCS) | NCSドメイン:
NCS oper: (Code: givenMatrix: (-0.982564198248, 0.0270791508129, -0.183941066409), (0.0306828012987, -0.952154748464, -0.304072196497), (-0.183374376686, -0.304414281152, 0.934722302829)ベクター: ...NCS oper: (Code: given Matrix: (-0.982564198248, 0.0270791508129, -0.183941066409), ベクター: |
-要素
#1: タンパク質 | 分子量: 22412.305 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOD2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04179, superoxide dismutase #2: 化合物 | #3: 化合物 | ChemComp-K / | #4: 化合物 | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | N | |
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-実験情報
-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: 2.57 Å3/Da / 溶媒含有率: 52.07 % |
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結晶化 | 温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.8 / 詳細: 1.93 M Potassium Phosphate |
-データ収集
回折 | 平均測定温度: 296 K / Serial crystal experiment: N |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU FR-E SUPERBRIGHT / 波長: 1.5418 Å |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2019年2月15日 |
放射 | モノクロメーター: Cu / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.16→50 Å / Num. obs: 25718 / % possible obs: 97.5 % / 冗長度: 7.6 % / Biso Wilson estimate: 30.18 Å2 / CC1/2: 0.804 / Net I/σ(I): 4.8 |
反射 シェル | 解像度: 2.16→2.2 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 953 / CC1/2: 0.638 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5VF9 解像度: 2.16→38.46 Å / SU ML: 0.2139 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 20.9831 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 34.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.16→38.46 Å
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拘束条件 |
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LS精密化 シェル |
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