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

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Basic information

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


Glycosphingolipid transport / synaptic vesicle budding / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the Golgi membrane / Golgi to transport vesicle transport / lysosomal membrane organization / Synthesis of PIPs at the plasma membrane / phospholipase D activator activity / trans-Golgi Network Vesicle Budding ...Glycosphingolipid transport / synaptic vesicle budding / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the Golgi membrane / Golgi to transport vesicle transport / lysosomal membrane organization / Synthesis of PIPs at the plasma membrane / phospholipase D activator activity / trans-Golgi Network Vesicle Budding / postsynaptic actin cytoskeleton organization / Intra-Golgi traffic / COPI-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of ER to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / mitotic cleavage furrow ingression / Lysosome Vesicle Biogenesis / very-low-density lipoprotein particle assembly / regulation of receptor internalization / MHC class II antigen presentation / regulation of Arp2/3 complex-mediated actin nucleation / Golgi Associated Vesicle Biogenesis / positive regulation of calcium ion-dependent exocytosis / dendritic spine organization / long-term synaptic depression / peroxisomal membrane / positive regulation of sodium ion transmembrane transport / positive regulation of dendritic spine development / cell leading edge / positive regulation of endocytosis / intracellular copper ion homeostasis / vesicle-mediated transport / endomembrane system / actin filament organization / sarcomere / small monomeric GTPase / positive regulation of protein secretion / intracellular protein transport / trans-Golgi network / GDP binding / late endosome / neuron projection / postsynaptic density / Golgi membrane / protein domain specific binding / GTPase activity / GTP binding / glutamatergic synapse / magnesium ion binding / Golgi apparatus / protein-containing complex / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Small GTPase Arf domain 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 domain 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 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
B: RAT ADP-RIBOSYLATION FACTOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3786
Polymers41,4432
Non-polymers9354
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-46 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 45.010, 91.960
Angle α, β, γ (deg.)90.00, 133.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20721.742 Da / Num. of mol.: 2
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.: 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.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURAL ELEMENTS HAVE BEEN NAMED TO PRESERVE THE ACCEPTED NOMENCLATURE FOR THE RAS SUPERFAMILY.
Nonpolymer detailsMAGNESIUM MAY NOT BE FULLY OCCUPIED OR MAY BE A WATER MOLECULE.

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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: 2.21 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
222 %PEG80001reservoir
30.2 Mammonium sulfate1reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 13030 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.01 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
Num. measured all: 40351

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.315 -5 %
Rwork0.187 --
obs0.187 12521 -
Displacement parametersBiso mean: 42.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 58 212 3118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.01
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

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