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Yorodumi- PDB-1td1: Crystal Structure of the Purine Nucleoside Phosphorylase from Sch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1td1 | ||||||
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Title | Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1td1.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1td1.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 1td1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1td1_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 1td1_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 1td1_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 1td1_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/1td1 ftp://data.pdbj.org/pub/pdb/validation_reports/td/1td1 | 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: 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: 40.6 % |
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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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2002 / Details: Si 111 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→54 Å / Num. all: 61501 / Num. obs: 58392 / % possible obs: 93.5 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.063 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SmPNP refined at 2.1 angstrons Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.516 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.3 / σ(I): 2.3 / ESU R: 0.174 / ESU R Free: 0.141 / 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: 22.692 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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