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Yorodumi- PDB-1jlr: STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jlr | ||||||
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Title | STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 MUTANT C128V | ||||||
Components | Uracil Phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / UPRTASE / GTP activated / tetramer | ||||||
Function / homology | Function and homology information uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / GTP binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Model details | URACIL PHOSPHORIBOSYLTRANSFERASE (E.C.2.4.2.9) | ||||||
Authors | Schumacher, M.A. / Bashor, C.J. / Otsu, K. / Zu, S. / Parry, R. / Ulmman, B. / Brennan, R.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jlr.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jlr.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jlr ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jlr | HTTPS FTP |
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-Related structure data
Related structure data | 1jlsC 1bd3S 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
#1: Protein | Mass: 27558.246 Da / Num. of mol.: 4 / Mutation: C1128V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pBACE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q26998, uracil phosphoribosyltransferase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GTP / #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: 2.52 Å3/Da / Density % sol: 51.21 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Citrate buffer, NaCl, Ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 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: 2.45→16.1 Å / Num. obs: 34646 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2240 / Rsym value: 0.143 / % possible all: 67 |
Reflection | *PLUS Num. measured all: 77473 |
Reflection shell | *PLUS Highest resolution: 2.4 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BD3 Resolution: 2.45→16.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 522583.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.5739 Å2 / ksol: 0.300439 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→16.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.184 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.1 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.326 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.276 |