- PDB-3dz8: Crystal structure of human Rab3B GTPase bound with GDP -
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基本情報
登録情報
データベース: PDB / ID: 3dz8
タイトル
Crystal structure of human Rab3B GTPase bound with GDP
要素
Ras-related protein Rab-3B
キーワード
PROTEIN TRANSPORT / ras / gdp / gtpase / structural genomics consortium / sgc / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Transport
機能・相同性
機能・相同性情報
positive regulation of dopamine uptake involved in synaptic transmission / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / regulation of exocytosis / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion ...positive regulation of dopamine uptake involved in synaptic transmission / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / regulation of exocytosis / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / synaptic vesicle membrane / GDP binding / synaptic vesicle / vesicle / endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytoplasm 類似検索 - 分子機能
Rab3 / small GTPase Rab1 family profile. / 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 ...Rab3 / small GTPase Rab1 family profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-3B 類似検索 - 構成要素
解像度: 1.9→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.204 / SU B: 8.566 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.153 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
反射数
%反射
Selection details
Rfree
0.251
763
4.903 %
RANDOM
Rwork
0.211
-
-
-
obs
0.213
15562
99.724 %
-
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 BULK SOLVENT
原子変位パラメータ
Biso mean: 15.646 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.208 Å2
0 Å2
-1.59 Å2
2-
-
1.537 Å2
0 Å2
3-
-
-
-1.464 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→20 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1390
0
34
30
1454
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1456
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
962
X-RAY DIFFRACTION
r_angle_refined_deg
1.381
1.955
1976
X-RAY DIFFRACTION
r_angle_other_deg
0.862
3
2330
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.644
5
179
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.192
23.636
66
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.066
15
240
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.515
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
221
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1618
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
324
X-RAY DIFFRACTION
r_mcbond_it
1.403
2
884
X-RAY DIFFRACTION
r_mcbond_other
0.415
2
364
X-RAY DIFFRACTION
r_mcangle_it
2.134
3
1419
X-RAY DIFFRACTION
r_scbond_it
1.684
2
572
X-RAY DIFFRACTION
r_scangle_it
2.368
3
556
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20