TRANSPORT PROTEIN / GTPase-GDP-metal-GEF complex / vps9 domain / Ras super family / guanine nucleotide exchange factor / small GTPase / GDP/GTP binding / divalent metal binding / geranylgeranylation
Function / homology
Function and homology information
cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / embryo development ending in seed dormancy / vacuole organization / late endosome to vacuole transport / molecular sequestering activity / multivesicular body membrane / small molecule binding ...cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / embryo development ending in seed dormancy / vacuole organization / late endosome to vacuole transport / molecular sequestering activity / multivesicular body membrane / small molecule binding / endocytic vesicle / GTPase activator activity / guanyl-nucleotide exchange factor activity / intracellular protein transport / small GTPase binding / early endosome membrane / early endosome / endosome / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 ...Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Serum Albumin; Chain A, Domain 1 / small GTPase Rab1 family profile. / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Vacuolar protein sorting-associated protein 9A / Ras-related protein RABF2b Similarity search - Component
Resolution: 2.2→55.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.882 / SU B: 6.454 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27282
1140
5.1 %
RANDOM
Rwork
0.19801
-
-
-
obs
0.20173
21156
99.89 %
-
all
-
21179
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 32.054 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.82 Å2
0 Å2
0 Å2
2-
-
1.5 Å2
0 Å2
3-
-
-
-0.69 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→55.73 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3171
0
29
261
3461
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
3260
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.374
1.964
4411
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.882
5
400
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.521
25.226
155
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.061
15
572
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.439
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
492
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2451
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.781
1.5
2007
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.507
2
3225
X-RAY DIFFRACTION
r_scbond_it
2.283
3
1253
X-RAY DIFFRACTION
r_scangle_it
3.844
4.5
1186
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.199→2.256 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.292
81
-
Rwork
0.22
1528
-
obs
-
1609
99.2 %
+
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