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Yorodumi- PDB-1g6y: CRYSTAL STRUCTURE OF THE GLOBULAR REGION OF THE PRION PROTEIN URE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g6y | ||||||
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Title | CRYSTAL STRUCTURE OF THE GLOBULAR REGION OF THE PRION PROTEIN URE2 FROM YEAST SACCHAROMYCES CEREVISIAE | ||||||
Components | URE2 PROTEIN | ||||||
Keywords | STRUCTURAL GENOMICS / GST SUPERFAMILY | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein urmylation / 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: 2.8 Å | ||||||
Authors | Bousset, L. / Belrhali, H. / Janin, J. / Melki, R. / Morera, S. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Structural Characterization of Saccharomyces cerevisiae Prion-like Protein Ure2 Authors: Thual, C. / Komar, A.A. / Bousset, L. / Fernandez-Bellot, E. / Cullin, C. / Melki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g6y.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g6y.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6y ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6y | 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: 29966.104 Da / Num. of mol.: 2 / Fragment: GLOBULAR DOMAIN (RESIDUES 94-354) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: URE2 OR YNL229C OR N1165 / Plasmid: PET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P23202 #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: 43.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Peg 1000, CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 24, 2000 |
Radiation | Monochromator: Asymmetric Laue C111 Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 14010 / Num. obs: 12931 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.341 / % possible all: 89.8 |
Reflection | *PLUS Num. measured all: 170419 |
Reflection shell | *PLUS % possible obs: 89.8 % / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.217 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.3 Å2 |