[English] 日本語
Yorodumi- PDB-2xbu: Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xbu | ||||||
---|---|---|---|---|---|---|---|
Title | Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with GMP (monoclinic crystal form) | ||||||
Components | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE / FLIP PEPTIDE-PLANE | ||||||
Function / homology | Function and homology information XMP salvage / hypoxanthine phosphoribosyltransferase / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / nucleus ...XMP salvage / hypoxanthine phosphoribosyltransferase / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Functional Significance of Four Successive Glycine Residues in the Pyrophosphate Binding Loop of Fungal 6-Oxopurine Phosphoribosyltransferases. Authors: Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A. #1: Journal: Genetics / Year: 2008 Title: Lethal Accumulation of Guanylic Nucleotides in Saccharomyces Cerevisiae Hpt1-Deregulated Mutants. Authors: Breton, A. / Pinson, B. / Coulpier, F. / Giraud, M. / Dautant, A. / Daignan-Fornier, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xbu.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xbu.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xbu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xbu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xbu_validation.xml.gz | 23 KB | Display | |
Data in CIF | 2xbu_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/2xbu ftp://data.pdbj.org/pub/pdb/validation_reports/xb/2xbu | HTTPS FTP |
-Related structure data
Related structure data | 2jkySC 2jkzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9848, 0.01737, 0.173), Vector: |
-Components
#1: Protein | Mass: 25223.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: Y1846 / Plasmid: PET-21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q04178, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.35 Å3/Da / Density % sol: 45.1 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 30% PEG 4000, 0.1 M TRI-SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 27, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.21 Å / Num. obs: 39543 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JKY Resolution: 1.8→28.214 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 19.97 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.25 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28.214 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|