+Open data
-Basic information
Entry | Database: PDB / ID: 1k0c | ||||||
---|---|---|---|---|---|---|---|
Title | Ure2p in complex with S-p-nitrobenzylglutathione | ||||||
Components | URE2 PROTEIN | ||||||
Keywords | GENE REGULATION / Nitrate assimilation / Structural genomics | ||||||
Function / homology | Function and homology information protein urmylation / Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / glutathione peroxidase / negative regulation of transcription by transcription factor localization / regulation of nitrogen utilization / glutathione peroxidase activity / nitrate assimilation / phosphoprotein binding / transcription corepressor activity / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bousset, L. / Belrhali, H. / Melki, R. / Morera, S. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structures of the yeast prion Ure2p functional region in complex with glutathione and related compounds. Authors: Bousset, L. / Belrhali, H. / Melki, R. / Morera, S. #1: Journal: Structure / Year: 2001 Title: Structure of the Globular Region of the Prion Protein Ure2 from the Yeast Saccharomyces cerevisiae Authors: Bousset, L. / Belrhali, H. / Janin, J. / Melki, R. / Morera, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k0c.cif.gz | 201 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k0c.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 1k0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k0c_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k0c_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1k0c_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 1k0c_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0c ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29834.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P23202 #2: Chemical | #3: Chemical | ChemComp-GSH / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.21 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: peg 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Bousset, L., (2001) Structure, 9, 39. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 40155 / Num. obs: 38381 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rsym value: 0.08 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 93.5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 94 % / Num. measured all: 390942 / Rmerge(I) obs: 0.08 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.214 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|