+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2sod | |||||||||
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タイトル | DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE | |||||||||
要素 | COPPER,ZINC SUPEROXIDE DISMUTASE | |||||||||
キーワード | OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) | |||||||||
機能・相同性 | 機能・相同性情報 neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / スーパーオキシドディスムターゼ / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / glutathione metabolic process / ovarian follicle development / 着床 / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / regulation of mitochondrial membrane potential / locomotory behavior / response to organic substance / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / 血圧 / ペルオキシソーム / protein polyubiquitination / ubiquitin-protein transferase activity / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / 精子形成 / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / ミトコンドリア / zinc ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Bos taurus (ウシ) | |||||||||
手法 | X線回折 / 解像度: 2 Å | |||||||||
データ登録者 | Tainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C. | |||||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1982 タイトル: Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. 著者: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C. #1: ジャーナル: Nature / 年: 1983 タイトル: Structure and Mechanism of Copper, Zinc Superoxide Dismutase 著者: Tainer, J.A. / Getzoff, E.D. / Richardson, J.S. / Richardson, D.C. #2: ジャーナル: Nature / 年: 1983 タイトル: Electrostatic Recognition between Superoxide and Copper, Zinc Superoxide Dismutase 著者: Getzoff, E.D. / Tainer, J.A. / Weiner, P.K. / Kollman, P.A. / Richardson, J.S. / Richardson, D.C. #3: ジャーナル: Biochemistry / 年: 1977 タイトル: Metal Sites of Copper-Zinc Superoxide Dismutase 著者: Beem, K.M. / Richardson, D.C. / Rajagopalan, K.V. #4: ジャーナル: J.Mol.Biol. / 年: 1976 タイトル: Similarity of Three-Dimensional Structure between the Immunoglobulin Domain and the Copper,Zinc Superoxide Dismutase Subunit 著者: Richardson, J.S. / Richardson, D.C. / Thomas, K.A. / Silverton, E.W. / Davies, D.R. #5: ジャーナル: Biochem.Biophys.Res.Commun. / 年: 1975 タイトル: Alpha-Carbon Coordinates for Bovine Cu,Zn Superoxide Dismutase 著者: Richardson, J.S. / Thomas, R.A. / Richardson, D.C. #6: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1975 タイトル: Crystal Structure of Bovine Cu,Zn Superoxide Dismutase at 3 Angstroms Resolution,Chain Tracing and Metal Ligands 著者: Richardson, J.S. / Thomas, K.A. / Rubin, B.H. / Richardson, D.C. #7: ジャーナル: J.Biol.Chem. / 年: 1974 タイトル: The Crystal Structure of Bovine Cu2+,Zn2+ Superoxide Dismutase at 5.5 Angstroms Resolution 著者: Thomas, K.A. / Rubin, B.H. / Bier, C.J. / Richardson, J.S. / Richardson, D.C. #8: ジャーナル: J.Biol.Chem. / 年: 1972 タイトル: Two Crystal Forms of Bovine Superoxide Dismutase 著者: Richardson, D.C. / Bier, C.J. / Richardson, J.S. | |||||||||
履歴 |
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Remark 700 | SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION ...SHEET EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A WATER MOLECULE. THE DOMINANT STRUCTURAL FEATURE OF EACH MONOMER IS AN EIGHT-STRANDED ANTI-PARALLEL BETA-BARREL. THERE ARE, HOWEVER, NO HYDROGEN BONDS BETWEEN STRANDS 4 AND 5. THIS BARREL IS DESCRIBED IN SHEET RECORDS BELOW AS A NINE-STRANDED SHEET WITH IDENTICAL FIRST AND LAST STRANDS. |
-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 | 2sod.cif.gz | 130.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2sod.ent.gz | 91.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2sod.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/so/2sod ftp://data.pdbj.org/pub/pdb/validation_reports/so/2sod | 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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2 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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詳細 | THE TRANSFORMATION WHICH WILL PLACE THE YELLOW MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 1 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE BLUE MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 2 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE GREEN MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 3 BELOW. |
-要素
#1: タンパク質 | 分子量: 15599.375 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) 参照: UniProt: P00442, スーパーオキシドディスムターゼ #2: 化合物 | ChemComp-CU / #3: 化合物 | ChemComp-ZN / #4: 水 | ChemComp-HOH / | |
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-実験情報
-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: 2.42 Å3/Da / 溶媒含有率: 49.13 % | ||||||||||||||||||||
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結晶化 | *PLUS pH: 7.5 / 手法: unknown | ||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
反射 | *PLUS 最高解像度: 2 Å / 最低解像度: 4 Å / Num. obs: 17206 / % possible obs: 35 % |
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-解析
ソフトウェア | 名称: PROLSQ / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | Rfactor Rwork: 0.256 / 最高解像度: 2 Å 詳細: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER ...詳細: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER COMPRISES MONOMERS BLUE (B) AND GREEN (G). ONLY THOSE HYDROGEN BONDS OF WHICH THE DEPOSITORS ARE MOST CERTAIN ARE PRESENTED ON THE CONECT RECORDS BELOW. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 2 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 4 Å / 最高解像度: 2 Å / Rfactor obs: 0.255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: o_bond_d / Dev ideal: 0.03 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS |