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Yorodumi- PDB-1vst: Symmetric Sulfolobus solfataricus uracil phosphoribosyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vst | ||||||
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Title | Symmetric Sulfolobus solfataricus uracil phosphoribosyltransferase with bound PRPP and GTP | ||||||
Components | Uracil phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / uracil / phosphoribosyltransferase / allosteric regulation / Sulfolobus solfataricus / PRPP / GTP / Glycosyltransferase / Magnesium | ||||||
Function / homology | Function and homology information uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / hypoxanthine phosphoribosyltransferase activity / UMP salvage / IMP salvage / GTP binding ...uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / GMP salvage / hypoxanthine phosphoribosyltransferase activity / UMP salvage / IMP salvage / GTP binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kadziola, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus Authors: Christoffersen, S. / Kadziola, A. / Johansson, E. / Rasmussen, M. / Willemoes, M. / Jensen, K.F. #1: Journal: Biochemistry / Year: 2005 Title: Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus. Authors: Arent, S. / Harris, P. / Jensen, K.F. / Larsen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vst.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vst.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vst ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vst | HTTPS FTP |
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-Related structure data
Related structure data | 3g6wC 1xtvS 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: 24179.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0231, upp / Plasmid: pLFS2 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830 References: UniProt: Q980Q4, uracil phosphoribosyltransferase |
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#2: Chemical | ChemComp-GTP / |
#3: Chemical | ChemComp-MG / |
#4: Sugar | ChemComp-PRP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG8000, 0.1M sodium-cacodylate, pH6.5, 200mM magnesium-chloride, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.954 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 22, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. all: 7102 / Num. obs: 7102 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XTV Resolution: 2.8→25 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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