- PDB-2hup: Crystal structure of human RAB43 in complex with GDP -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2hup
Title
Crystal structure of human RAB43 in complex with GDP
Components
RAS-related protein RAB-43
Keywords
SIGNALING PROTEIN / G-PROTEIN / RAB / GDP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information
retrograde transport, plasma membrane to Golgi / phagosome maturation / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / phagocytic vesicle / trans-Golgi network membrane ...retrograde transport, plasma membrane to Golgi / phagosome maturation / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / phagocytic vesicle / trans-Golgi network membrane / intracellular protein transport / cellular response to type II interferon / phagocytic vesicle membrane / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain ...: / : / 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 Similarity search - Domain/homology
BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.
Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.213 / SU B: 5.608 / SU ML: 0.156 / Cross valid method: FREE R / ESU R: 0.233 / ESU R Free: 0.208 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLPROBITY HAS ALSO BEEN USED FOR REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2862
2019
8.428 %
thin shells
Rwork
0.2331
-
-
-
all
0.237
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-
-
obs
-
23955
99.688 %
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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: 24.248 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.984 Å2
0.492 Å2
0 Å2
2-
-
0.984 Å2
0 Å2
3-
-
-
-1.477 Å2
Refinement step
Cycle: LAST / Resolution: 2.05→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2455
0
61
76
2592
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2554
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1665
X-RAY DIFFRACTION
r_angle_refined_deg
1.41
1.973
3464
X-RAY DIFFRACTION
r_angle_other_deg
0.966
3
4049
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.13
5
314
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.986
23.398
103
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.451
15
424
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.568
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
406
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2787
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
544
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
469
X-RAY DIFFRACTION
r_nbd_other
0.199
0.2
1686
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
1220
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1268
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
105
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.164
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.218
0.2
74
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.157
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
2.402
2
1645
X-RAY DIFFRACTION
r_mcbond_other
0.715
2
651
X-RAY DIFFRACTION
r_mcangle_it
3.291
3
2525
X-RAY DIFFRACTION
r_scbond_it
2.377
2
1103
X-RAY DIFFRACTION
r_scangle_it
3.087
3
939
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 (%)
2.05-2.103
0.383
166
0.268
1552
0.28
1728
99.421
2.103-2.16
0.284
161
0.237
1538
0.241
1699
100
2.16-2.222
0.278
173
0.224
1473
0.23
1651
99.697
2.222-2.289
0.361
169
0.247
1391
0.258
1586
98.361
2.289-2.363
0.262
103
0.222
1436
0.225
1542
99.805
2.363-2.445
0.357
32
0.223
1470
0.226
1506
99.734
2.445-2.536
0.286
133
0.207
1317
0.214
1452
99.862
2.536-2.637
0.263
131
0.224
1262
0.228
1397
99.714
2.637-2.752
0.271
120
0.227
1245
0.231
1367
99.854
2.752-2.884
0.298
134
0.239
1162
0.245
1299
99.769
2.884-3.037
0.309
164
0.223
1062
0.234
1230
99.675
3.037-3.216
0.31
72
0.226
1074
0.231
1148
99.826
3.216-3.432
0.252
72
0.219
1037
0.221
1111
99.82
3.432-3.698
0.239
60
0.194
984
0.197
1047
99.713
3.698-4.037
0.233
101
0.191
849
0.196
951
99.895
4.037-4.491
0.176
59
0.176
828
0.176
888
99.887
4.491-5.142
0.221
43
0.217
756
0.217
799
100
5.142-6.196
0.394
59
0.301
625
0.309
684
100
6.196-8.371
0.413
31
0.343
533
0.347
564
100
8.371-20
0.411
36
0.394
342
0.396
381
99.213
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