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Yorodumi- PDB-5kap: Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kap | ||||||
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Title | Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with a 9-(4-(phosphonobutil)hypoxanthine | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / complex / dimer / enzyme / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / nuclear lumen / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / glycosome / nuclear lumen / ciliary plasm / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Teran, D. / Guddat, L. | ||||||
Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kap.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kap.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/5kap ftp://data.pdbj.org/pub/pdb/validation_reports/ka/5kap | HTTPS FTP |
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-Related structure data
Related structure data | 5jsqSC 5jv5C 5k51C 5kamC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli) References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: 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: 2.4 Å3/Da / Density % sol: 48.74 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 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: 2.81→47.39 Å / Num. obs: 11686 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.81→2.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JSQ Resolution: 2.95→45.106 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.56 / 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: 2.95→45.106 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: -36.4196 Å / Origin y: 32.7608 Å / Origin z: 23.6149 Å
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Refinement TLS group | Selection details: all |