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Yorodumi- PDB-1tcv: Crystal Structure of the Purine Nucleoside Phosphorylase from Sch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tcv | ||||||
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Title | Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with Non-detergent Sulfobetaine 195 and acetate | ||||||
Components | purine-nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Purine Nucleoside Phosphorylase | ||||||
Function / homology | Function and homology information nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Pereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structures for the Potential Drug Target Purine Nucleoside Phosphorylase from Schistosoma mansoni Causal Agent of Schistosomiasis. Authors: Pereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Cloning, expression and preliminary crystallographic studies of the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni Authors: Pereira, H.M. / Cleasby, A. / Pena, S.D. / Franco, G.R. / Garratt, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tcv.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tcv.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tcv_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 1tcv_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 1tcv_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 1tcv_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tcv ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tcv | HTTPS FTP |
-Related 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: 31197.254 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SmPNP / Plasmid: pMal C2g / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: Q9BMI9, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 277 K / pH: 5 Details: PEG 1500, Glycerol, acetete buffer, Non-detergent sulfobetaine 195, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2001 |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.5 Å / Num. obs: 78422 / % possible obs: 99.3 % / Observed criterion σ(I): 2.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.081 |
Reflection shell | Resolution: 1.75→1.84 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.298 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The starting model for molecular replacement was the SmPNP (purine nucleoside phosphorylase from S. mansoni) refined at 2.75 A resolution. Resolution: 1.75→87.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.261 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDIN
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→87.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20 /
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