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Yorodumi- PDB-6bif: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bif | ||||||
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Title | Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 1-(4-amino-2-hydroxyphenyl)ethan-1-one | ||||||
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: 1.6 Å | ||||||
Authors | Faheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 1-(4-amino-2-hydroxyphenyl)ethan-1-one Authors: Faheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bif.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bif.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 6bif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bif_validation.pdf.gz | 732.7 KB | Display | wwPDB validaton report |
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Full document | 6bif_full_validation.pdf.gz | 733.9 KB | Display | |
Data in XML | 6bif_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 6bif_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bif ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bif | HTTPS FTP |
-Related structure data
Related structure data | 5cxqS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31435.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 (DE3) References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase | ||||
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#2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-DSJ / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.32 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Ammonium Acetate , 0.1 M Bis-Tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→57.62 Å / Num. obs: 43879 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3199 / CC1/2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CXQ Resolution: 1.6→57.62 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→57.62 Å
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Refine LS restraints |
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LS refinement shell |
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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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