+Open data
-Basic information
Entry | Database: PDB / ID: 5xbv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Wss1 mutant from saccharomyces cerevisiae | ||||||
Components | Wss1p | ||||||
Keywords | HYDROLASE / protease | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.804 Å | ||||||
Authors | Dong, Y.H. / Yang, X.Y. / Wang, W.J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: crystal structure of Wss1 mutant from saccharomyces cerevisiae Authors: Dong, Y.H. / Yang, X.Y. / Wang, W.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xbv.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xbv.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xbv_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xbv_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 5xbv_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 5xbv_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/5xbv ftp://data.pdbj.org/pub/pdb/validation_reports/xb/5xbv | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17444.383 Da / Num. of mol.: 1 / Fragment: UNP residues 2-149 / Mutation: E116Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: FostersO / Gene: FOSTERSO_2154 / Production host: Escherichia coli (E. coli) / References: UniProt: E7NIN2 |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 44.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10%(w/v) PEG-8000, 20mM Tris-HCl, pH 7.0, and 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 14399 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Net I/σ(I): 35.98 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 702 / CC1/2: 0.922 / Rpim(I) all: 0.171 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.804→24.884 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.82 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.804→24.884 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -28.9539 Å / Origin y: 3.4725 Å / Origin z: 2.9354 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |