- PDB-1z6x: Structure Of Human ADP-Ribosylation Factor 4 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1z6x
Title
Structure Of Human ADP-Ribosylation Factor 4
Components
ADP-ribosylation factor 4ADP ribosylation factor
Keywords
TRANSPORT PROTEIN / GDP-BINDING / MEMBRANE TRAFFICKING / GOLGI STACK / LIPOPROTEIN / MYRISTATE / Structural Genomics / PSI / Protein Structure Initiative / Structural Genomics Consortium / SGC
Function / homology
Function and homology information
: / activation of phospholipase D activity / VxPx cargo-targeting to cilium / dendritic spine development / apical protein localization / protein localization to cilium / establishment or maintenance of epithelial cell apical/basal polarity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / regulation of postsynapse organization / regulation of reactive oxygen species metabolic process ...: / activation of phospholipase D activity / VxPx cargo-targeting to cilium / dendritic spine development / apical protein localization / protein localization to cilium / establishment or maintenance of epithelial cell apical/basal polarity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / regulation of postsynapse organization / regulation of reactive oxygen species metabolic process / COPI-dependent Golgi-to-ER retrograde traffic / epidermal growth factor receptor binding / cilium assembly / response to axon injury / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / learning / intracellular protein transport / brain development / epidermal growth factor receptor signaling pathway / ruffle membrane / cell migration / dendritic spine / GTPase activity / glutamatergic synapse / GTP binding / negative regulation of apoptotic process / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function
small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.7→32.38 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27269
466
4.8 %
RANDOM
Rwork
0.22166
-
-
-
obs
0.22419
9184
99.84 %
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all
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9651
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-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 40.803 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.18 Å2
0 Å2
0 Å2
2-
-
1.18 Å2
0 Å2
3-
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-2.37 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→32.38 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2800
0
58
55
2913
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
2906
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.226
1.988
3944
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.124
5
348
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
43.67
24.615
130
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.955
15
528
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.82
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.07
0.2
456
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2112
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.23
0.2
1519
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.311
0.2
1988
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.161
0.2
141
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
0.236
0.2
75
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.291
0.2
6
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
0.605
1.5
1730
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.102
2
2796
X-RAY DIFFRACTION
r_scbond_it
0.799
3
1176
X-RAY DIFFRACTION
r_scangle_it
1.348
4.5
1148
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.385
27
-
Rwork
0.295
642
-
obs
-
-
100 %
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