- PDB-2p5s: RAB domain of human RASEF in complex with GDP -
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Basic information
Entry
Database: PDB / ID: 2p5s
Title
RAB domain of human RASEF in complex with GDP
Components
RAS and EF-hand domain containing
Keywords
SIGNALING PROTEIN / G-PROTEIN / RAB / GDP / STRUCTURAL GENOMICS / SGC / Structural Genomics Consortium
Function / homology
Function and homology information
vesicle-mediated transport / GDP binding / GTPase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / identical protein binding / cytosol Similarity search - Function
: / 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 / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif ...: / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
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.
Resolution: 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 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. arp/warp, molprobity, coot were also used for the refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2602
1377
5.617 %
thin shells
Rwork
0.2111
-
-
-
all
0.214
-
-
-
obs
-
24513
99.106 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
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
Refinement step
Cycle: LAST / Resolution: 2.15→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2430
0
59
38
2527
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
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 refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
% reflection obs (%)
2.15-2.205
0.333
188
0.277
1486
0.283
1775
94.31
2.205-2.265
0
0.281
1693
0.281
1750
96.743
2.265-2.33
0.322
184
0.276
1500
0.282
1711
98.422
2.33-2.4
0
0.245
1636
0.245
1641
99.695
2.4-2.478
0.303
152
0.244
1468
0.25
1625
99.692
2.478-2.563
0
0.257
1536
0.257
1542
99.611
2.563-2.658
0.283
140
0.223
1388
0.228
1528
100
2.658-2.765
0.277
98
0.222
1326
0.226
1425
99.93
2.765-2.885
0.395
5
0.222
1378
0.222
1385
99.856
2.885-3.023
0.308
111
0.22
1238
0.227
1350
99.926
3.023-3.183
0.249
100
0.212
1168
0.215
1275
99.451
3.183-3.37
0
0.201
1201
0.201
1201
100
3.37-3.596
0.25
73
0.199
1078
0.202
1152
99.913
3.596-3.873
0.249
76
0.188
975
0.192
1052
99.905
3.873-4.227
0.263
59
0.178
933
0.182
994
99.799
4.227-4.7
0.134
47
0.164
840
0.162
890
99.663
4.7-5.378
0.265
52
0.174
760
0.179
812
100
5.378-6.471
0.242
30
0.229
652
0.229
682
100
6.471-8.707
0.224
40
0.206
536
0.208
576
100
8.707-20
0.24
22
0.219
344
0.22
368
99.457
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