- PDB-2gao: Crystal Structure of Human SAR1a in Complex With GDP -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 2gao
タイトル
Crystal Structure of Human SAR1a in Complex With GDP
要素
GTP-binding protein SAR1a
キーワード
PROTEIN TRANSPORT / gtpase / structural genomics consortium / gdp / SGC
機能・相同性
機能・相同性情報
amino acid sensor activity / regulation of COPII vesicle coating / cellular response to leucine starvation / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coating / membrane organization ...amino acid sensor activity / regulation of COPII vesicle coating / cellular response to leucine starvation / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coating / membrane organization / Golgi cisterna membrane / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of TORC1 signaling / small monomeric GTPase / G protein activity / intracellular protein transport / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / cytosol 類似検索 - 分子機能
small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 / Small COPII coat GTPase SAR1A 類似検索 - 構成要素
解像度: 2→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.191 / SU B: 5.341 / SU ML: 0.146 / ESU R: 0.188 / ESU R Free: 0.175 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ARP/wARP by LAMZIN,PERRAKIS,MORRIS was also used for refinement
Rfactor
反射数
%反射
Selection details
Rfree
0.2694
1470
5.067 %
thin shells
Rwork
0.2238
-
-
-
all
0.226
-
-
-
obs
-
29010
99.227 %
-
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: 1.4 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータ
Biso mean: 18.669 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.914 Å2
0 Å2
0.138 Å2
2-
-
-1.376 Å2
0 Å2
3-
-
-
0.538 Å2
精密化ステップ
サイクル: LAST / 解像度: 2→30 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2661
0
58
61
2780
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2764
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1861
X-RAY DIFFRACTION
r_angle_refined_deg
1.422
2.007
3742
X-RAY DIFFRACTION
r_angle_other_deg
0.953
3
4560
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.935
5
334
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.112
24.375
112
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.564
15
508
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.716
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
437
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2952
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
542
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
491
X-RAY DIFFRACTION
r_nbd_other
0.187
0.2
1917
X-RAY DIFFRACTION
r_nbtor_refined
0.173
0.2
1306
X-RAY DIFFRACTION
r_nbtor_other
0.082
0.2
1327
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.156
0.2
91
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.261
0.2
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.205
0.2
41
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.066
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
2.71
2
2160
X-RAY DIFFRACTION
r_mcbond_other
0.605
2
692
X-RAY DIFFRACTION
r_mcangle_it
3.217
3
2682
X-RAY DIFFRACTION
r_scbond_it
2.218
2
1301
X-RAY DIFFRACTION
r_scangle_it
3.019
3
1058
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20