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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: 1cyf | ||||||
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タイトル | IDENTIFYING THE PHYSIOLOGICAL ELECTRON TRANSFER SITE OF CYTOCHROME C PEROXIDASE BY STRUCTURE-BASED ENGINEERING | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE (H2O2(A)) | ||||||
機能・相同性 | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() | ||||||
![]() | Miller, M.A. / Han, G.W. / Kraut, J. | ||||||
![]() | ![]() タイトル: Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering. 著者: Miller, M.A. / Geren, L. / Han, G.W. / Saunders, A. / Beasley, J. / Pielak, G.J. / Durham, B. / Millett, F. / Kraut, J. #1: ![]() タイトル: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis 著者: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J. #2: ![]() タイトル: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution 著者: Finzel, B.C. / Poulos, T.L. / Kraut, J. | ||||||
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 | ![]() | 77.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 57.9 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 472.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 489.6 KB | 表示 | |
XML形式データ | ![]() | 10.1 KB | 表示 | |
CIF形式データ | ![]() | 15.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | |
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類似構造データ |
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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: 33769.605 Da / 分子数: 1 / 変異: INS(MET ILE AT N-TERMINUS), C128A, A193C / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() |
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#2: 化合物 | ChemComp-HEM / |
#3: 水 | ChemComp-HOH / |
構成要素の詳細 | THE SIDE CHAIN AT CYS 193 IS DISORDERED, AND NO INTERPRETABLE DENSITY WAS FOUND BEYOND SG OF CYS ...THE SIDE CHAIN AT CYS 193 IS DISORDERED |
配列の詳細 | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM A PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ENTRY ...THIS CYTOCHROME |
-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: 2.49 Å3/Da / 溶媒含有率: 50.66 % |
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結晶化 | *PLUS 手法: unknown |
-データ収集
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
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解析
ソフトウェア | 名称: TNT / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 解像度: 2.35→20 Å / Isotropic thermal model: 0 / σ(F): 0 立体化学のターゲット値: D.E. TRONRUD ET AL., ACTA CRYST. A43, 489 (1987) 詳細: THE ADDITION OF A BULKY GROUP AT POSITION 193 MAKES IT IMPOSSIBLE FOR THE ENZYME TO CRYSTALLIZE IN A FORM THAT IS ISOMORPHOUS WITH THE CCP(MI) PARENT. THIS IS BECAUSE CB OF ALA 193 IN THE ...詳細: THE ADDITION OF A BULKY GROUP AT POSITION 193 MAKES IT IMPOSSIBLE FOR THE ENZYME TO CRYSTALLIZE IN A FORM THAT IS ISOMORPHOUS WITH THE CCP(MI) PARENT. THIS IS BECAUSE CB OF ALA 193 IN THE PARENT MAKES A CRYSTAL CONTACT WITH THE SIDE CHAIN OF THR 275. THE MUTANT ENZYME ADOPTS A NEW CRYSTAL PACKING THAT ALLOWS RESIDUE 193 TO PROJECT INTO AN OTHERWISE UNOCCUPIED AREA. THE MODEL WAS CREATED INITIALLY USING MOLECULAR REPLACEMENT WITH THE CCP(MI) PARENT AS THE SEARCH MODEL. TRANSLATION FUNCTIONS WERE CALCULATED BY SAMPLING A TRANSLATION VECTOR ON A 1 ANGSTROM GRID, UTILIZING DATA BETWEEN 8 AND 4 ANGSTROM RESOLUTION. THE TRANSLATION VECTOR WAS FURTHER REFINED BY AN R-FACTOR MINIMIZATION PROCEDURE WITH STEPS OF 0.1 ANGSTROM, RESULTING IN AN R-FACTOR OF 0.283 FOR DATA TO 4 ANGSTROMS RESOLUTION. UNLIKE THE CCP(MI) PARENT, COORDINATES FOR RESIDUES -1, 0, AND 1 - 3 ARE INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. WATER MOLECULES WITH B-FACTORS GREATER THAN 80. WERE NOT INCLUDED.
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溶媒の処理 | 溶媒モデル: MOEW & KRETSINGER, JMB 91, 211-228 (1975) / Bsol: 91.17 Å2 / ksol: 0.67 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.35→20 Å
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拘束条件 |
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