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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: 3e8z | ||||||
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タイトル | X-ray structure of rat arginase I-N130A mutant: the unliganded complex | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE / Amino Acid Recognition / arginase / mutant N130A / Arginine metabolism / Cytoplasm / Manganese / Metal-binding / Phosphoprotein / Urea cycle | ||||||
機能・相同性 | ![]() regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity / arginine catabolic process to ornithine / negative regulation of type II interferon-mediated signaling pathway / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / cellular response to interleukin-4 / cellular response to dexamethasone stimulus / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / lung development / liver development / female pregnancy / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / adaptive immune response / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Shishova, E.Y. / Di Costanzo, L. / Christianson, D.W. | ||||||
![]() | ![]() タイトル: Probing the specificity determinants of amino acid recognition by arginase. 著者: Shishova, E.Y. / Di Costanzo, L. / Emig, F.A. / Ash, D.E. / Christianson, D.W. | ||||||
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 | ![]() | 188.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 149.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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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: 34976.070 Da / 分子数: 3 / 変異: N130A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #2: 化合物 | ChemComp-MN / #3: 水 | ChemComp-HOH / | |
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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: 2.11 Å3/Da / 溶媒含有率: 41.67 % |
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 詳細: drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M ...詳細: drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M NaCl] were equilibrated over a 1 mL reservoir of precipitant solution., VAPOR DIFFUSION, HANGING DROP |
-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: ADSC QUANTUM 210 / 検出器: CCD |
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 Å / 相対比: 1 |
反射 | 解像度: 2→60.4 Å / Num. all: 53201 / Num. obs: 53201 / % possible obs: 91.8 % / 冗長度: 2.9 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.3 |
反射 シェル | 解像度: 2→2.1 Å / 冗長度: 1.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3 / Num. unique all: 5603 / % possible all: 66.1 |
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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: 1RLA 解像度: 2→41.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2364867.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 56.7599 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
原子変位パラメータ | Biso mean: 25.5 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2→41.77 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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