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- PDB-1jls: STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE URACIL/CPR 2 MU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jls | ||||||
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Title | STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE URACIL/CPR 2 MUTANT C128V | ||||||
![]() | Uracil phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / UPRTASE / ternary complex / UPRT-cprpp-uracil | ||||||
Function / homology | ![]() ribosylnicotinamide kinase activity / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / chloroplast / GTP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Bashor, C.J. / Otsu, K. / Zu, S. / Parry, R. / Ullman, B. / Brennan, R.G. | ||||||
![]() | ![]() Title: The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase. Authors: Schumacher, M.A. / Bashor, C.J. / Song, M.H. / Otsu, K. / Zhu, S. / Parry, R.J. / Ullman, B. / Brennan, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.1 KB | Display | ![]() |
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PDB format | ![]() | 151.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.6 KB | Display | ![]() |
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Full document | ![]() | 991.3 KB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jlrC ![]() 1bd3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 5 molecules BADC![](data/chem/img/PRP.gif)
![](data/chem/img/PRP.gif)
#1: Protein | Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C128V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q26998, uracil phosphoribosyltransferase #5: Sugar | ChemComp-PRP / | |
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-Non-polymers , 4 types, 132 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-URA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: NaCl, citrate/phosphate buffer, PEG 3400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.7 | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 23, 1994 / Details: yale mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→60 Å / Num. obs: 32692 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4008 / Rsym value: 0.265 / % possible all: 56 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 60 Å / Num. measured all: 99823 |
Reflection shell | *PLUS Highest resolution: 2.5 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BD3 Resolution: 2.5→60.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1115798.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 89.708 Å2 / ksol: 0.342656 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 58.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→60.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.265 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.1 Å2 | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.409 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.372 |