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Yorodumi- PDB-3e9z: Crystal structure of purine nucleoside phosphorylase from Schisto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e9z | ||||||
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Title | Crystal structure of purine nucleoside phosphorylase from Schistosoma mansoni in complex with 6-chloroguanine | ||||||
Components | Purine-nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Schistosoma Purine Nucleoside Phosphorylase / Glycosyltransferase | ||||||
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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.31 Å | ||||||
Authors | Pereira, H.M. / Rezende, M.M. / Oliva, G. / Garratt, R.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase (SmPNP) in complex with adenine, 8-aminoguanine, 8-azaguanine and 6-chloroguanine. Authors: Pereira, H.M. / Rezende, M.M. / Oliva, G. / 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 | 3e9z.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e9z.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 3e9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e9z_validation.pdf.gz | 502.4 KB | Display | wwPDB validaton report |
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Full document | 3e9z_full_validation.pdf.gz | 527.1 KB | Display | |
Data in XML | 3e9z_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 3e9z_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9z ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9z | HTTPS FTP |
-Related structure data
Related structure data | 1td1S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
-Protein , 1 types, 3 molecules ABC
#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 |
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-Non-polymers , 5 types, 690 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 1.91 Å3/Da / Density % sol: 35.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 18-20% PEG 1500, 20% Glycerol, 32mM Sodium acetate, VAPOR DIFFUSION, temperature 277K PH range: 4.9-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→129.05 Å / Num. obs: 30649 / % possible obs: 95.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.93 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1TD1 Resolution: 2.31→56.629 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.759 Å2 / ksol: 0.375 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.31 Å2 / Biso mean: 27.4 Å2 / Biso min: 8.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→56.629 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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