+Open data
-Basic information
Entry | Database: PDB / ID: 4goc | ||||||
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Title | Crystal structure of the Get5 ubiquitin-like domain | ||||||
Components | Golgi to ER traffic protein 5 | ||||||
Keywords | PROTEIN BINDING / ubiquitin-like domain / protein-protein interaction / Sgt2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chartron, J.W. / VanderVelde, D.G. / Clemons Jr., W.M. | ||||||
Citation | Journal: Cell Rep / Year: 2012 Title: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface. Authors: Chartron, J.W. / Vandervelde, D.G. / 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 | 4goc.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4goc.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4goc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4goc ftp://data.pdbj.org/pub/pdb/validation_reports/go/4goc | HTTPS FTP |
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-Related structure data
Related structure data | 2lxaC 2lxbC 2lxcC 4godC 4goeC 4gofC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8544.010 Da / Num. of mol.: 3 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: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo(DE3) / References: UniProt: Q12285 #2: 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: 2.19 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING 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: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2012 |
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: 2.4→29.07 Å / Num. obs: 9092 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.8 / Num. unique all: 666 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.069 Å / SU ML: 0.39 / σ(F): 2.03 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.069 Å
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Refine LS restraints |
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LS refinement shell |
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