+Open data
-Basic information
Entry | Database: PDB / ID: 1s4u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure analysis of the beta-propeller protein Ski8p | ||||||
Components | Antiviral protein SKI8Antiviral drug | ||||||
Keywords | ANTIVIRAL PROTEIN / WD repeat | ||||||
Function / homology | Function and homology information Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / protein-containing complex assembly ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / protein-containing complex assembly / defense response to virus / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Cheng, Z. / Song, H. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination Authors: Cheng, Z. / Liu, Y. / Wang, C. / Parker, R. / Song, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1s4u.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1s4u.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4u ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4u | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45222.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SKI8, YGL213C / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Ril / References: UniProt: Q02793 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG4000, Sodium citrate, Ethylene glycol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9789, 0.9791, 0.9724 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2003 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.1→20 Å / Num. all: 21453 / Num. obs: 21439 / % possible obs: 0.999 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||
Reflection shell | Resolution: 2.1→2.154 Å / % possible all: 0.988 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.315 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.319 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.711 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
|