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Yorodumi- PDB-2jky: SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANS... -
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-Basic information
Entry | Database: PDB / ID: 2jky | ||||||
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Title | SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (GUANOSINE 5'- MONOPHOSPHATE) (TETRAGONAL CRYSTAL FORM) | ||||||
Components | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / NUCLEUS / MAGNESIUM / GMP COMPLEX / FLIP PEPTIDE-PLANE / GLYCOSYLTRANSFERASE / METAL-BINDING / PURINE SALVAGE | ||||||
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 / MAD / Resolution: 2.3 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. #2: Journal: J.Mol.Biol. / Year: 1998 Title: Structures of Free and Complexed Forms of Escherichia Coli Xanthine-Guanine Phosphoribosyltransferase. Authors: Vos, S. / Parry, R.J. / Burns, M.R. / De Jersey, J. / Martin, J.L. #3: Journal: Biochemistry / Year: 1997 Title: Crystal Structure of Escherichia Coli Xanthine Phosphoribosyltransferase. Authors: Vos, S. / De Jersey, J. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jky.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jky.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jky_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2jky_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2jky_validation.xml.gz | 18 KB | Display | |
Data in CIF | 2jky_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/2jky ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jky | HTTPS FTP |
-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: 24213.590 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-214 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 / | |
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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: 2.31 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 30% PEG 4000, 0.1 M TRI-SODIUM CITRATE PH 5.6, IN MICROBATCH UNDER OIL, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 26, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) SINGLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 20429 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.94 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.92 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.3→30.27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.449 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30.27 Å
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