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- PDB-1rrf: NON-MYRISTOYLATED RAT ADP-RIBOSYLATION FACTOR-1 COMPLEXED WITH GD... -

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Basic information

Entry
Database: PDB / ID: 1rrf
TitleNON-MYRISTOYLATED RAT ADP-RIBOSYLATION FACTOR-1 COMPLEXED WITH GDP, MONOMERIC CRYSTAL FORM
ComponentsRAT ADP-RIBOSYLATION FACTOR-1
KeywordsTRANSPORT PROTEIN / GDP-BINDING / MEMBRANE TRAFFICKING
Function / homology
Function and homology information


Synthesis of PIPs at the Golgi membrane / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the plasma membrane / Golgi to transport vesicle transport / phospholipase D activator activity / Intra-Golgi traffic / COPI-dependent Golgi-to-ER retrograde traffic ...Synthesis of PIPs at the Golgi membrane / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the plasma membrane / Golgi to transport vesicle transport / phospholipase D activator activity / Intra-Golgi traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / trans-Golgi Network Vesicle Budding / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / positive regulation of calcium ion-dependent exocytosis / postsynaptic actin cytoskeleton organization / dendritic spine organization / long-term synaptic depression / positive regulation of dendritic spine development / positive regulation of sodium ion transmembrane transport / positive regulation of endocytosis / cell leading edge / intracellular copper ion homeostasis / endomembrane system / vesicle-mediated transport / sarcomere / small monomeric GTPase / actin filament organization / positive regulation of protein secretion / intracellular protein transport / GDP binding / late endosome / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / 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 / P-loop containing nucleoside triphosphate hydrolase ...ADP-ribosylation factor 1-5 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsGreasley, S.E. / Jhoti, H. / Bax, B.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: The structure of rat ADP-ribosylation factor-1 (ARF-1) complexed to GDP determined from two different crystal forms.
Authors: Greasley, S.E. / Jhoti, H. / Teahan, C. / Solari, R. / Fensome, A. / Thomas, G.M. / Cockcroft, S. / Bax, B.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies on Adp-Ribosylation Factor 1
Authors: Greasley, S. / Jhoti, H. / Fensome, A.C. / Cockcroft, S. / Thomas, G.M. / Bax, B.
History
DepositionDec 16, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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

Downloads & links

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Assembly

Deposited unit
A: RAT ADP-RIBOSYLATION FACTOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1893
Polymers20,7221
Non-polymers4682
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.700, 45.250, 60.450
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RAT ADP-RIBOSYLATION FACTOR-1 / ARF-


Mass: 20721.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P84079
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Compound detailsSECONDARY STRUCTURAL ELEMENTS HAVE BEEN NAMED TO PRESERVE THE ACCEPTED NOMENCLATURE FOR THE RAS SUPERFAMILY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.29 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.05 Msodium citrate1drop
310 %(v/v)2-propanol1drop
410 %PEG40001drop
50.1 Msodium citrate1reservoir
620 %(v/v)2-propanol1reservoir
720 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→21 Å / Num. obs: 3415 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Num. measured all: 7676

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 3→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.319 -
Rwork0.231 -
obs0.231 3191
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 29 0 1407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.341

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