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Yorodumi- PDB-4zkd: Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zkd | ||||||
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Title | Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate. | ||||||
Components | Superkiller protein 7 | ||||||
Keywords | GTP-BINDING PROTEIN / GTPase / translation / NGD / Ski / hydrolase | ||||||
Function / homology | Function and homology information Eukaryotic Translation Elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation ...Eukaryotic Translation Elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / protein catabolic process / protein-macromolecule adaptor activity / translation / GTPase activity / protein-containing complex binding / GTP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.181 Å | ||||||
Authors | Kowalinski, E. / Conti, E. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases. Authors: Kowalinski, E. / Schuller, A. / Green, R. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zkd.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zkd.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 4zkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/4zkd ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zkd | 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: 56658.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SKI7, YOR076C, YOR29-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08491 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Hepes pH 7.0, 700mM NaH2PO4/K2HPO4, 3% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.181→73.72 Å / Num. obs: 59361 / % possible obs: 99.71 % / Redundancy: 6.6 % / Net I/σ(I): 15.98 |
Reflection shell | Resolution: 2.181→2.259 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.86 / % possible all: 97.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.181→73.717 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 34.79 / 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: 2.181→73.717 Å
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Refine LS restraints |
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LS refinement shell |
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