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- PDB-5knt: Crystal structure of E. coli hypoxanthine phosphoribosyltransfera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5knt | ||||||
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Title | Crystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with 2-((2,3-Dihydroxypropyl)(2-(hypoxanthin-9-yl)ethyl)amino)ethylphosphonic acid | ||||||
![]() | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE/INHIBITOR / Acyclic nucleoside phosphonate / EcHPRT / phosphoribosyltransferase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization ...hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / nucleotide binding / magnesium ion binding / protein-containing complex / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eng, W.S. / Keough, D.T. / Hockova, D. / Janeba, Z. | ||||||
![]() | ![]() Title: Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase Authors: Eng, W.S. / Hockova, D. / Spacek, P. / Baszczynski, O. / Janeba, Z. / Naesens, L. / Keough, D.T. / Guddat, L.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5knrC ![]() 5knsC ![]() 5knuC ![]() 5knvC ![]() 5knxC ![]() 1g9sS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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Unit cell |
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Components
#1: Protein | Mass: 20643.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5 and 0.1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→44.3 Å / Num. obs: 23337 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G9S Resolution: 2.55→44.3 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.54 Å2 / Biso mean: 51.9658 Å2 / Biso min: 23.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→44.3 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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