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- PDB-3lgo: Structure of Gse1p, member of the GSE/EGO complex -

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Basic information

Entry
Database: PDB / ID: 3lgo
TitleStructure of Gse1p, member of the GSE/EGO complex
ComponentsProtein SLM4
KeywordsPROTEIN BINDING / Roadblock/LC7 / domain swap / Autophagy / Membrane / Transmembrane / Transport / Vacuole
Function / homology
Function and homology information


Ragulator complex / microautophagy / endocytic recycling / fungal-type vacuole membrane / positive regulation of TOR signaling / late endosome membrane / late endosome / protein transport / signal transduction / identical protein binding / cytoplasm
Similarity search - Function
GSE/EGO complex subunit Slm4 / Protein SLM4 / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsKogan, K. / Fass, D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural conservation of components in the amino acid sensing branch of the TOR pathway in yeast and mammals.
Authors: Kogan, K. / Spear, E.D. / Kaiser, C.A. / Fass, D.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SLM4


Theoretical massNumber of molelcules
Total (without water)19,5631
Polymers19,5631
Non-polymers00
Water362
1
A: Protein SLM4

A: Protein SLM4

A: Protein SLM4

A: Protein SLM4


Theoretical massNumber of molelcules
Total (without water)78,2534
Polymers78,2534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area12530 Å2
ΔGint-83 kcal/mol
Surface area25080 Å2
MethodPISA
2
A: Protein SLM4

A: Protein SLM4


Theoretical massNumber of molelcules
Total (without water)39,1262
Polymers39,1262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3780 Å2
ΔGint-31 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.290, 73.290, 147.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Protein SLM4 / GSE complex subunit 1 / EGO complex subunit 3


Mass: 19563.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EGO3, GSE1, SLM4, YBR0723, YBR077C / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38247
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 100 mM sodium citrate buffer, pH 2.0, 500-800 mM ammonium sulfate, 200 mM lithium sulfate, 200-350 mM L-arginine-HCl, pH 5.75, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 5995 / Num. obs: 5873 / % possible obs: 98.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 83.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 13.8
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.949 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.85→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.351 463 -random
Rwork0.317 ---
all-5949 --
obs-5862 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 2 1094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.587

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