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Yorodumi- PDB-1xtv: Sulfolobus solfataricus uracil phosphoribosyltransferase with uri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xtv | ||||||
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Title | Sulfolobus solfataricus uracil phosphoribosyltransferase with uridine 5'-monophosphate (UMP) bound to half of the subunits | ||||||
Components | Probable uracil phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Tetramer / type 1 phosphoribosyltransferase / UMP complex | ||||||
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: 2.6 Å | ||||||
Authors | Arent, S. / Harris, P. / Jensen, K.F. / Larsen, S. | ||||||
Citation | 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 | 1xtv.cif.gz | 334 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xtv.ent.gz | 275.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xtv ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xtv | HTTPS FTP |
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-Related structure data
Related structure data | 1xttSC 1xtuC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24179.348 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: upp / Plasmid: pUHE23-2 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830 References: UniProt: Q980Q4, uracil phosphoribosyltransferase #2: Chemical | ChemComp-U5P / |
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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: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.133 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 10, 2002 / Details: Bent mirror |
Radiation | Monochromator: Si(III) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.133 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 55389 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.098 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 1.3 / Num. unique all: 4840 / Rsym value: 0.397 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Sulfolobus solfataricus UPRTase PDB ID 1XTT Resolution: 2.6→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.4 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.034
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