+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 3e9b | ||||||
---|---|---|---|---|---|---|---|
タイトル | X-ray structure of rat arginase I-T135A mutant: the complex with BEC | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE / amino acid recognition / arginase mutant / T135A / BEC / Arginine metabolism / 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 / response to selenium ion / arginase / 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 / response to selenium ion / arginase / arginase activity / arginine catabolic process to ornithine / 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 / negative regulation of type II interferon-mediated signaling pathway / 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 / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / 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 / nucleus / 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 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 191.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 151.4 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 | ![]() | 455 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 478.4 KB | 表示 | |
XML形式データ | ![]() | 39.6 KB | 表示 | |
CIF形式データ | ![]() | 55.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
要素
#1: タンパク質 | 分子量: 34989.070 Da / 分子数: 3 / 変異: T135A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #2: 化合物 | ChemComp-MN / #3: 化合物 | #4: 水 | ChemComp-HOH / | |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.12 Å3/Da / 溶媒含有率: 41.99 % |
---|---|
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 8000] were ...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 8000] 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 |
---|---|
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 | 相対比: 1 |
反射 | 解像度: 2.15→50 Å / Num. all: 46355 / Num. obs: 46355 / % possible obs: 98.8 % / 冗長度: 3.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.2 |
反射 シェル | 解像度: 2.15→2.25 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4254 / % possible all: 91.2 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 1RLA 解像度: 2.15→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 71054.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 53.8251 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.15→50 Å
| ||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.15→2.28 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|