[English] 日本語
Yorodumi- PDB-2isc: Crystal structure of Purine Nucleoside Phosphorylase from Trichom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2isc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A | ||||||
Components | purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase | ||||||
Function / homology | Function and homology information uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol Similarity search - Function | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rinaldo-Matthis, A. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues Authors: Rinaldo-Matthis, A. / Wing, C. / Ghanem, M. / Deng, H. / Wu, P. / Gupta, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Almo, S.C. / Wang, C.C. / Schramm, V.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2isc.cif.gz | 275.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2isc.ent.gz | 223.3 KB | Display | PDB format |
PDBx/mmJSON format | 2isc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isc ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isc | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the functional hexameric unit |
-Components
#1: Protein | Mass: 26366.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: A2E7Y6, purine-nucleoside phosphorylase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-223 / ( #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.17 M Sodium Acetate, 25.5% PEG 4000, 0.085 M TrisHCL, 15% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979099 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2006 |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979099 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 51179 / Num. obs: 50207 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 50.856 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.116 / Χ2: 0.597 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.72 / Num. unique all: 4713 / Rsym value: 0.594 / Χ2: 0.561 / % possible all: 93.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.99 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.382 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.872 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
|