- PDB-2g77: Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase... -
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基本情報
登録情報
データベース: PDB / ID: 2g77
タイトル
Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3
要素
GTPase-activating protein GYP1
Ras-related protein Rab-33B
キーワード
HYDROLASE ACTIVATOR/PROTEIN TRANSPORT / Protein transport / Gyp1 TBC domain / Rab33 / vesicular trafficking / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT COMPLEX
機能・相同性
機能・相同性情報
negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / Intra-Golgi traffic / regulation of Golgi organization / Rab protein signal transduction / protein localization to Golgi apparatus / intra-Golgi vesicle-mediated transport / regulation of exocytosis ...negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / Intra-Golgi traffic / regulation of Golgi organization / Rab protein signal transduction / protein localization to Golgi apparatus / intra-Golgi vesicle-mediated transport / regulation of exocytosis / Golgi stack / skeletal system morphogenesis / autophagosome assembly / vesicle-mediated transport / GTPase activator activity / Golgi lumen / protein transport / presynapse / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / mitochondrion 類似検索 - 分子機能
Rab33A/B / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / small GTPase Rab1 family profile. / Cyclin A; domain 1 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Rab33A/B / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / small GTPase Rab1 family profile. / Cyclin A; domain 1 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-33B / GTPase-activating protein GYP1 類似検索 - 構成要素
解像度: 2.26→2.34 Å / 冗長度: 5.1 % / Mean I/σ(I) obs: 4.93 / Num. unique all: 6309 / Rsym value: 0.354 / % possible all: 99.9
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0005
精密化
DENZO
データ削減
SCALEPACK
データスケーリング
SHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.26→8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.205 / SU ML: 0.155 / 交差検証法: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.218 / 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
0.24357
1634
5.1 %
RANDOM
Rwork
0.20524
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all
0.207
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obs
0.20726
30553
98.65 %
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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