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- PDB-2jky: SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANS... -
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Open data
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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) | ||||||
![]() | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / NUCLEUS / MAGNESIUM / GMP COMPLEX / FLIP PEPTIDE-PLANE / GLYCOSYLTRANSFERASE / METAL-BINDING / PURINE SALVAGE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: Y1846 / Plasmid: PET-21 / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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