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- PDB-1fzq: CRYSTAL STRUCTURE OF MURINE ARL3-GDP -

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Basic information

Entry
Database: PDB / ID: 1fzq
TitleCRYSTAL STRUCTURE OF MURINE ARL3-GDP
ComponentsADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3
KeywordsSIGNALING PROTEIN / Protein-GDP complex without magnesium / ARF family / Ras Superfamily / G-domain
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / ciliary transition zone / intraciliary transport / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport / protein localization to cilium / smoothened signaling pathway ...Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / ciliary transition zone / intraciliary transport / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport / protein localization to cilium / smoothened signaling pathway / small GTPase-mediated signal transduction / axoneme / mitotic cytokinesis / cilium assembly / cytoplasmic microtubule / ciliary basal body / kidney development / spindle microtubule / cilium / GDP binding / microtubule cytoskeleton / protein transport / midbody / microtubule binding / Golgi membrane / GTPase activity / centrosome / GTP binding / Golgi apparatus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
ADP-ribosylation factor-like protein 2/3 / 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-like protein 2/3 / 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 / AMMONIUM ION / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHillig, R.C. / Hanzal-Bayer, M. / Linari, M. / Becker, J. / Wittinghofer, A. / Renault, L.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Structural and biochemical properties show ARL3-GDP as a distinct GTP binding protein.
Authors: Hillig, R.C. / Hanzal-Bayer, M. / Linari, M. / Becker, J. / Wittinghofer, A. / Renault, L.
#1: Journal: FEBS Lett. / Year: 1999
Title: The Delta Subunit of Rod Specific Cyclic GMP Phophodiesterase, PDE Delta, Interacts with the Arf-like Protein Arl3 in a GTP Specific Manner
Authors: Linari, M. / Hanzal-Bayer, M. / Becker, J.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-LIKE PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2296
Polymers20,3801
Non-polymers8495
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.421, 64.583, 40.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological active unit is most probably a monomer. The electron density map showed a disulphide bridge between Cys 118 and a symmetry-related Cys 118 of a crystal neighbour. This is considered to be a crystallization artefact and was not included in the model.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3 / ARF-LIKE PROTEIN 3 / ARL3


Mass: 20380.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUL7

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulphate, MES, magnesium chloride, DTE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
129 mg/mlprotein1drop
21.60-1.96 Mammonium sulfate1reservoir
3MES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 1.7→29.62 Å / Num. all: 22084 / Num. obs: 22047 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1098 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human ARF1-GDP, PDB ENTRY 1HUR

1hur


Resolution: 1.7→29.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114931615.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2005 9.1 %RANDOM
Rwork0.213 ---
all0.215 22047 --
obs0.215 22047 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.72 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å20 Å2
2--0.6 Å20 Å2
3---1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 51 163 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 326 9.1 %
Rwork0.236 3271 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GDP.PARAMGDP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5MES.PARAMMES.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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