- PDB-2p5s: RAB domain of human RASEF in complex with GDP -
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基本情報
登録情報
データベース: PDB / ID: 2p5s
タイトル
RAB domain of human RASEF in complex with GDP
要素
RAS and EF-hand domain containing
キーワード
SIGNALING PROTEIN / G-PROTEIN (Gタンパク質) / RAB / GDP / STRUCTURAL GENOMICS (構造ゲノミクス) / SGC / Structural Genomics Consortium
機能・相同性
機能・相同性情報
vesicle-mediated transport / GDP binding / GTPase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / identical protein binding / 細胞質基質 類似検索 - 分子機能
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 / 低分子量GTPアーゼ / 低分子量GTPアーゼ / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...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 / 低分子量GTPアーゼ / 低分子量GTPアーゼ / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / ロスマンフォールド / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / Ras and EF-hand domain-containing protein 類似検索 - 構成要素
BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.
解像度: 2.15→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.195 / SU B: 5.428 / SU ML: 0.142 / ESU R: 0.204 / ESU R Free: 0.189 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. arp/warp, molprobity, coot were also used for the refinement
Rfactor
反射数
%反射
Selection details
Rfree
0.2602
1377
5.617 %
thin shells
Rwork
0.2111
-
-
-
all
0.214
-
-
-
obs
-
24513
99.106 %
-
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: 27.035 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.075 Å2
0 Å2
0.194 Å2
2-
-
0.951 Å2
0 Å2
3-
-
-
-0.816 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.15→20 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2430
0
59
38
2527
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
2524
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1679
X-RAY DIFFRACTION
r_angle_refined_deg
1.423
1.987
3409
X-RAY DIFFRACTION
r_angle_other_deg
0.924
3
4091
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.801
5
312
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.547
24.059
101
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.017
15
438
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.877
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
392
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2746
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
516
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
427
X-RAY DIFFRACTION
r_nbd_other
0.184
0.2
1641
X-RAY DIFFRACTION
r_nbtor_refined
0.173
0.2
1182
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
1254
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.121
0.2
77
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.12
0.2
4
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.247
0.2
18
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.147
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
2.911
2
1759
X-RAY DIFFRACTION
r_mcbond_other
0.647
2
653
X-RAY DIFFRACTION
r_mcangle_it
3.723
3
2489
X-RAY DIFFRACTION
r_scbond_it
2.447
2
1082
X-RAY DIFFRACTION
r_scangle_it
3.354
3
920
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20