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Yorodumi- PDB-7cmj: Crystal structure of L.donovani Hypoxanthine-guanine phosphoribos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cmj | ||||||
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Title | Crystal structure of L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT) | ||||||
Components | Hypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / hypoxanthine / guanine / phosphoribosyl / complex / tetramer. | ||||||
Function / homology | Function and homology information hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Parihar, P.S. / Pratap, J.V. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: The L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT) oligomer is distinct from the human homolog. Authors: Parihar, P.S. / Pratap, J.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cmj.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cmj.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/7cmj ftp://data.pdbj.org/pub/pdb/validation_reports/cm/7cmj | HTTPS FTP |
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-Related structure data
Related structure data | 1pzmS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23642.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: unlined residue have missing electron density, side chain of some residue also missing are with removed side chain. Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote) Strain: BPK282A1 / Gene: LDBPK_210980 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: E9BF84, hypoxanthine phosphoribosyltransferase |
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-Non-polymers , 7 types, 120 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PG4 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.64 Å3/Da / Density % sol: 70.39 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium cacodylate, 0.2 M Ammonium sulfate, 20% PEG 4000 PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9784 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019 / Details: Monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→44.373 Å / Num. obs: 17049 / % possible obs: 93.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 52.65 Å2 / Rmerge(I) obs: 0.04166 / Net I/σ(I): 10.15 |
Reflection shell | Resolution: 2.76→2.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2919 / Num. unique obs: 1731 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PZM Resolution: 2.76→44.37 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / 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: 2.76→44.37 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: -31.4031 Å / Origin y: 31.0988 Å / Origin z: -11.5201 Å
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Refinement TLS group | Selection details: ALL |