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Yorodumi- PDB-1tcu: Crystal Structure of the Purine Nucleoside Phosphorylase from Sch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tcu | ||||||
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Title | Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with phosphate and acetate | ||||||
Components | purine-nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Purine Nucleoside Phosphorylase | ||||||
Function / homology | Function and homology information guanosine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / Rigid Body / Resolution: 2 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 | 1tcu.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tcu.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tcu_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 1tcu_full_validation.pdf.gz | 488.3 KB | Display | |
Data in XML | 1tcu_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 1tcu_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tcu ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tcu | 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: Chemical | #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: 2.1 Å3/Da / Density % sol: 40.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 1500, Glycerol, Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2003 / Details: mirrors |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.82 Å / Num. obs: 50988 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Rsym value: 0.071 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.39 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Starting model: SmPNP refined at 1.9 angstrons Resolution: 2→25.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.201 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.226 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.515 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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