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Yorodumi- PDB-1bd3: STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bd3 | ||||||
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Title | STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V | ||||||
Components | URACIL PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / UPRTASE | ||||||
Function / homology | Function and homology information ribosylnicotinamide kinase activity / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / chloroplast / GTP binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.93 Å | ||||||
Authors | Schumacher, M.A. / Carter, D. / Scott, D. / Roos, D. / Ullman, B. / Brennan, R.G. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. Authors: Schumacher, M.A. / Carter, D. / Scott, D.M. / Roos, D.S. / Ullman, B. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bd3.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bd3.ent.gz | 156.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bd3_validation.pdf.gz | 417.3 KB | Display | wwPDB validaton report |
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Full document | 1bd3_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 1bd3_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 1bd3_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/1bd3 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bd3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THERE ARE FOUR MONOMERS (CHAINS A, B, C, D) IN THE ASYMMETRIC UNIT. THESE MONOMERS MAKE UP THE UPRTASE TETRAMER. |
-Components
#1: Protein | Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C128V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q26998, uracil phosphoribosyltransferase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Nonpolymer details | THE STRUCTURE HAS TWO PHOSPHATE MOLECULES (USED IN CRYSTALLIZATION). ONE PHOSPHATE FOUND IN THE ...THE STRUCTURE HAS TWO PHOSPHATE MOLECULES (USED IN CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Detector | Date: Aug 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.93 Å |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 75978 / % possible obs: 92 % / Num. measured all: 178298 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Highest resolution: 1.93 Å / Lowest resolution: 2.07 Å / Mean I/σ(I) obs: 2.4 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.93→10 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.93→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_bond_d / Dev ideal: 0.014 |