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Yorodumi- PDB-2vfa: Crystal structure of a chimera of Plasmodium falciparum and human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vfa | ||||||
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Title | Crystal structure of a chimera of Plasmodium falciparum and human hypoxanthine-guanine phosphoribosyl transferases | ||||||
Components | HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE, HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / HYPOXANTHINE-GUANINE PHOSPHORIBOSYL TRANSFERASE (HGPRT) / PURINE SALVAGE / DISEASE MUTATION / GLYCOSYLTRANSFERASE / METAL-BINDING / GOUT / CHIMERA / MAGNESIUM | ||||||
Function / homology | Function and homology information xanthine phosphoribosyltransferase / adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / XMP salvage / xanthine phosphoribosyltransferase activity / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation ...xanthine phosphoribosyltransferase / adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / XMP salvage / xanthine phosphoribosyltransferase activity / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / 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 / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gayathri, P. / Selvi, T.S. / Subbayya, I.N.S. / Ashok, C.S. / Balaram, H. / Murthy, M.R.N. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal Structure of a Chimera of Human and Plasmodium Falciparum Hypoxanthine Guanine Phosphoribosyltransferases Provides Insights Into Oligomerization. Authors: Gayathri, P. / Sujay Subbayya, I.N. / Ashok, C.S. / Selvi, T.S. / Balaram, H. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vfa.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vfa.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vfa ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vfa | HTTPS FTP |
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-Related structure data
Related structure data | 1hmpS S: Starting model for refinement |
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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: 25832.939 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-56,49-160,171-231 Source method: isolated from a genetically manipulated source Details: CHIMERA OF HUMAN AND PLASMODIUM FALCIPARUM HGPRTS Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum), (gene. exp.) HOMO SAPIENS (human) Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SF609 References: UniProt: P20035, UniProt: P00492, Transferases; Glycosyltransferases; Pentosyltransferases, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: 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: 3.47 Å3/Da / Density % sol: 64.6 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M TRIS PH 8.0, 2.0M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 17, 2003 / Details: OSMIC MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 17496 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 13 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HMP Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / SU B: 28.988 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 54.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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