+Open data
-Basic information
Entry | Database: PDB / ID: 3lgo | ||||||
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Title | Structure of Gse1p, member of the GSE/EGO complex | ||||||
Components | Protein SLM4 | ||||||
Keywords | PROTEIN 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 / protein transport / late endosome / late endosome membrane / signal transduction / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | ||||||
Authors | Kogan, K. / Fass, D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lgo.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lgo.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lgo_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 3lgo_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 3lgo_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 3lgo_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/3lgo ftp://data.pdbj.org/pub/pdb/validation_reports/lg/3lgo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.85→2.9 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.949 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Resolution: 2.85→50 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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