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- PDB-1z6x: Structure Of Human ADP-Ribosylation Factor 4 -

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Basic information

Entry
Database: PDB / ID: 1z6x
TitleStructure Of Human ADP-Ribosylation Factor 4
ComponentsADP-ribosylation factor 4
KeywordsTRANSPORT 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


phospholipase D activator activity / regulation of cilium assembly / NAD+-protein-arginine ADP-ribosyltransferase activity / VxPx cargo-targeting to cilium / dendritic spine development / apical protein localization / protein localization to cilium / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / establishment or maintenance of epithelial cell apical/basal polarity / regulation of reactive oxygen species metabolic process ...phospholipase D activator activity / regulation of cilium assembly / NAD+-protein-arginine ADP-ribosyltransferase activity / VxPx cargo-targeting to cilium / dendritic spine development / apical protein localization / protein localization to cilium / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / establishment or maintenance of epithelial cell apical/basal polarity / regulation of reactive oxygen species metabolic process / COPI-dependent Golgi-to-ER retrograde traffic / regulation of postsynapse organization / epidermal growth factor receptor binding / cilium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / learning / intracellular protein transport / ruffle membrane / cell migration / dendritic spine / Golgi membrane / GTPase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / 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 / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / 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 / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChoe, J. / Atanassova, A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure Of Human ADP-Ribosylation Factor 4
Authors: Atanassova, A. / Choe, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 4
B: ADP-ribosylation factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0006
Polymers41,0652
Non-polymers9354
Water99155
1
A: ADP-ribosylation factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0003
Polymers20,5331
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0003
Polymers20,5331
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.770, 64.770, 155.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ADP-ribosylation factor 4


Mass: 20532.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF4 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18085
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: sodium citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2005 / Details: CONFOCAL MAXFLUX
RadiationMonochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→32.38 Å / Num. all: 9676 / Num. obs: 9676 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUR

1hur


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
RfactorNum. reflection% reflectionSelection details
Rfree0.27269 466 4.8 %RANDOM
Rwork0.22166 ---
obs0.22419 9184 99.84 %-
all-9651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.803 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--1.18 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 58 55 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9883944
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1245348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.6724.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95515528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.821518
X-RAY DIFFRACTIONr_chiral_restr0.070.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21519
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21988
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.51730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10222796
X-RAY DIFFRACTIONr_scbond_it0.79931176
X-RAY DIFFRACTIONr_scangle_it1.3484.51148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 27 -
Rwork0.295 642 -
obs--100 %

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