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- PDB-1moz: ADP-ribosylation factor-like 1 (ARL1) from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 1moz
TitleADP-ribosylation factor-like 1 (ARL1) from Saccharomyces cerevisiae
ComponentsADP-ribosylation factor-like protein 1
KeywordsPROTEIN BINDING / GTP-BINDING
Function / homology
Function and homology information


trans-Golgi network membrane organization / Retrograde transport at the Trans-Golgi-Network / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to Golgi apparatus / protein localization to phagophore assembly site / protein targeting to vacuole / protein-containing complex localization / Golgi to plasma membrane protein transport / phagophore assembly site / cellular response to nitrogen starvation ...trans-Golgi network membrane organization / Retrograde transport at the Trans-Golgi-Network / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to Golgi apparatus / protein localization to phagophore assembly site / protein targeting to vacuole / protein-containing complex localization / Golgi to plasma membrane protein transport / phagophore assembly site / cellular response to nitrogen starvation / vesicle-mediated transport / response to endoplasmic reticulum stress / macroautophagy / intracellular protein transport / trans-Golgi network / endocytosis / cellular response to heat / endosome membrane / GTPase activity / GTP binding / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
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 ...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-like protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsAmor, J.C. / Horton, J.R. / Zhu, X. / Wang, Y. / Sullards, C. / Ringe, D. / Cheng, X. / Kahn, R.A.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Structures of Yeast ARF2 and ARL1: DISTINCT ROLES FOR THE N TERMINUS IN THE STRUCTURE AND FUNCTION OF ARF FAMILY GTPases
Authors: Amor, J.C. / Horton, J.R. / Zhu, X. / Wang, Y. / Sullards, C. / Ringe, D. / Cheng, X. / Kahn, R.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1-binding proteins.
Authors: Van Valkenburgh, H. / Shern, J.F. / Sharer, J.D. / Zhu, X. / Kahn, R.A.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Characterization of an ADP-ribosylation factor-like 1 protein in Saccharomyces cerevisiae.
Authors: Lee, F.J. / Huang, C.F. / Yu, W.L. / Buu, L.M. / Lin, C.Y. / Huang, M.C. / Moss, J. / Vaughan, M.
History
DepositionSep 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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 1
B: ADP-ribosylation factor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7954
Polymers40,9092
Non-polymers8862
Water28816
1
A: ADP-ribosylation factor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8982
Polymers20,4541
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8982
Polymers20,4541
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.250, 104.250, 45.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ADP-ribosylation factor-like protein 1 / ARL1


Mass: 20454.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38116
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: polyethylene glycol 8000, TRIS, GDP, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
215 %glycerol1reservoir
30.1 MTris1reservoirpH8.5
41 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 30, 1999 / Details: first generation Osmic multilayer
RadiationMonochromator: Confocal Multilayer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.17→28 Å / Num. all: 9420 / Num. obs: 9179 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16
Reflection shellResolution: 3.17→3.22 Å / Rmerge(I) obs: 0.217 / Num. unique all: 453 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 28 Å / Num. measured all: 30535

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Processing

Software
NameClassification
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RRF

1rrf


Resolution: 3.17→28 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2458 959 RANDOM
Rwork0.206 --
all0.25 9179 -
obs0.24 8220 -
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-28 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3.17→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 56 16 2738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 3.17→3.22 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.3346 39 -
Rwork0.3177 --
obs-453 93 %
Refinement
*PLUS
Lowest resolution: 28 Å / Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS

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