+Open data
-Basic information
Entry | Database: PDB / ID: 3vej | ||||||
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Title | Crystal structure of the Get5 carboxyl domain from S. cerevisiae | ||||||
Components | Ubiquitin-like protein MDY2 | ||||||
Keywords | PROTEIN BINDING / alpha helical / dimerization / homodimerization | ||||||
Function / homology | Function and homology information cell morphogenesis involved in conjugation with cellular fusion / TRC complex / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å | ||||||
Authors | Chartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons Jr., W.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Get5 Carboxyl-terminal Domain Is a Novel Dimerization Motif That Tethers an Extended Get4/Get5 Complex. Authors: Chartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vej.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vej.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/3vej ftp://data.pdbj.org/pub/pdb/validation_reports/ve/3vej | 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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Details | The biological assembly is the dimer in the asymmetric unit. |
-Components
#1: Protein/peptide | Mass: 4734.325 Da / Num. of mol.: 2 / Fragment: carboxyl domain residues 175-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: GET5, MDY2, TMA24, YOL111C / Plasmid: pET-33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q12285 #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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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: 1.72 Å3/Da / Density % sol: 28.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 3.4 M ammonium sulfate, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→46.34 Å / Num. obs: 18288 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 11.91 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.63 |
Reflection shell | Resolution: 1.23→1.26 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1302 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.23→24.839 Å / SU ML: 0.2 / Isotropic thermal model: Mixed isotropic and anisotropic / σ(F): 1.39 / Phase error: 20.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.409 Å2 / ksol: 0.394 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.23→24.839 Å
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Refine LS restraints |
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LS refinement shell |
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