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Yorodumi- PDB-3ggc: Human hypoxanthine-guanine phosphoribosyltransferase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ggc | ||||||
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Title | Human hypoxanthine-guanine phosphoribosyltransferase in complex with 9-(2-phosphonoethoxyethyl)hypoxanthine | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / purine salvage / phosphoribosyltransferase / acyclic nucleoside phosphonate / Disease mutation / Glycosyltransferase / Gout / Magnesium / Metal-binding | ||||||
Function / homology | Function and homology information adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / IMP metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / GMP salvage / Purine salvage / IMP salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / purine ribonucleoside salvage / Azathioprine ADME / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.78 Å | ||||||
Authors | Guddat, L.W. / Keough, D.T. / Jersey, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Inhibition of hypoxanthine-guanine phosphoribosyltransferase by acyclic nucleoside phosphonates: a new class of antimalarial therapeutics. Authors: Keough, D.T. / Hockova, D. / Holy, A. / Naesens, L.M. / Skinner-Adams, T.S. / Jersey, J. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ggc.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ggc.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ggc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ggc_validation.pdf.gz | 934.4 KB | Display | wwPDB validaton report |
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Full document | 3ggc_full_validation.pdf.gz | 950.2 KB | Display | |
Data in XML | 3ggc_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 3ggc_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/3ggc ftp://data.pdbj.org/pub/pdb/validation_reports/gg/3ggc | HTTPS FTP |
-Related structure data
Related structure data | 3gepSC 3ggjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24481.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT, HPRT1, HPT / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606 References: UniProt: P00492, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.67 % |
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Crystal grow | pH: 6.5 Details: 0.1M citrate, 10% iso-propanol, 29% PEG 4000, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→111.11 Å / Num. all: 10911 / Num. obs: 10911 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2.78→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 15.6 / Num. unique all: 1080 / Rsym value: 0.254 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3GEP Resolution: 2.78→37.59 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 35.44 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.667 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→37.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.781→2.853 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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