- PDB-8tk3: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidi... -
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基本情報
登録情報
データベース: PDB / ID: 8tk3
タイトル
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites
要素
Dual specificity protein phosphatase 3
キーワード
HYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE / VHR
機能・相同性
機能・相同性情報
MAP kinase phosphatase activity / negative regulation of chemotaxis / protein tyrosine/serine/threonine phosphatase activity / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade ...MAP kinase phosphatase activity / negative regulation of chemotaxis / protein tyrosine/serine/threonine phosphatase activity / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade / myosin phosphatase activity / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / phosphatase activity / dephosphorylation / immunological synapse / peptidyl-tyrosine dephosphorylation / cellular response to epidermal growth factor stimulus / cytoskeletal protein binding / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine kinase binding / negative regulation of cell migration / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm 類似検索 - 分子機能
Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like 類似検索 - ドメイン・相同性
: / Dual specificity protein phosphatase 3 類似検索 - 構成要素
温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the ...詳細: The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the crystallization buffer. The crystals were soaked with 25 mM of the compound in solution (10% DMSO, 100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000).
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: 0.9201 Å / 相対比: 1
反射
解像度: 1.78→50.25 Å / Num. obs: 17972 / % possible obs: 99.3 % / 冗長度: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5
反射 シェル
解像度: 1.78→1.81 Å / 冗長度: 4 % / Num. unique obs: 1234 / CC1/2: 0.37 / % possible all: 96.1
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0411
精密化
autoPROC
データ削減
Aimless
データスケーリング
MOLREP
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 2→40.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.093 / SU ML: 0.181 / 交差検証法: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.188 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.25538
632
5 %
RANDOM
Rwork
0.18617
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obs
0.18968
12090
99.45 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK