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- PDB-5jv5: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jv5 | ||||||
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Title | Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with Guanosine 5' monophosphate | ||||||
![]() | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / complex / dimer / enzyme | ||||||
Function / homology | ![]() hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / nuclear lumen / IMP salvage / glycosome / ciliary plasm ...hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / nuclear lumen / IMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Teran, D. / Guddat, L. | ||||||
![]() | ![]() Title: Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase. Authors: Teran, D. / Hockova, D. / Cesnek, M. / Zikova, A. / Naesens, L. / Keough, D.T. / Guddat, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.3 KB | Display | ![]() |
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PDB format | ![]() | 126.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jsqSC ![]() 5k51C ![]() 5kamC ![]() 5kapC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 24221.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris PH range: 5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→48.01 Å / Num. obs: 13262 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.16 / Net I/av σ(I): 8.6 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.73→2.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JSQ Resolution: 2.73→48.011 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→48.011 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.9585 Å / Origin y: 27.784 Å / Origin z: 14.7837 Å
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Refinement TLS group | Selection details: all |