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Yorodumi- PDB-5euc: The role of the C-terminal region on the oligomeric state and enz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5euc | ||||||
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Title | The role of the C-terminal region on the oligomeric state and enzymatic activity of Trypanosoma cruzi hypoxanthine phosphoribosyl transferase | ||||||
Components | Hypoxanthine-guanine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / HPRT / phosphoribosyltransferase / T. cruzi / quaternary structure / enzymatic activity modulation / stability / proteolysis / reversible oligomerization / disorder C-terminal region / bisphosphonates | ||||||
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 | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Valsecchi, W.M. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Delfino, J.M. / Santos, J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2016 Title: The role of the C-terminal region on the oligomeric state and enzymatic activity of Trypanosoma cruzi hypoxanthine phosphoribosyl transferase. Authors: Valsecchi, W.M. / Cousido-Siah, A. / Defelipe, L.A. / Mitschler, A. / Podjarny, A. / Santos, J. / Delfino, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5euc.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5euc.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 5euc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5euc ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5euc | HTTPS FTP |
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-Related structure data
Related structure data | 1tc2S 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
#1: Protein | Mass: 26666.559 Da / Num. of mol.: 4 / Fragment: UNP residues 21-241 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053509693.70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4DRC4 #2: 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: 1.87 Å3/Da / Density % sol: 34.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: The drop was a 1:1 mix of protein (in tris 20 mM pH8, NaCl 100 mM) and buffer (1.0 mM MES buffer pH 6.5 and 12 % W/V of PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2012 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→36.34 Å / Num. all: 22566 / Num. obs: 22531 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TC2 Resolution: 2.65→36.34 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2491 / WRfactor Rwork: 0.1813 / FOM work R set: 0.8079 / SU B: 13.459 / SU ML: 0.279 / SU Rfree: 0.3889 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.72 Å2 / Biso mean: 44.54 Å2 / Biso min: 21.13 Å2
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Refinement step | Cycle: final / Resolution: 2.65→36.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.648→2.717 Å / Total num. of bins used: 20
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