+Open data
-Basic information
Entry | Database: PDB / ID: 4fuw | ||||||
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Title | Crystal structure of Ego3 mutant | ||||||
Components | Protein SLM4 | ||||||
Keywords | PROTEIN BINDING / EGO complex / Ego3 / TOR signaling | ||||||
Function / homology | Function and homology information Ragulator complex / microautophagy / endocytic recycling / fungal-type vacuole membrane / positive regulation of TOR signaling / late endosome / protein transport / late endosome membrane / signal transduction / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhang, T. / Peli-Gulli, M.P. / Yang, H. / De Virgilio, C. / Ding, J. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Ego3 functions as a homodimer to mediate the interaction between Gtr1-Gtr2 and Ego1 in the ego complex to activate TORC1. Authors: Zhang, T. / Peli-Gulli, M.P. / Yang, H. / De Virgilio, C. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fuw.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fuw.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/4fuw ftp://data.pdbj.org/pub/pdb/validation_reports/fu/4fuw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18367.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: SLM4, EGO3, GSE1, YBR077C, YBR0723 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P38247 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | RESIDUES 21-31 DLHSVDFKTS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M ammonium sulfate, 0.1M MES monohydrate, 10% 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 12915 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.103 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.846 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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