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- PDB-4d98: Crystal structure of the hexameric purine nucleoside phosphorylas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d98 | ||||||
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Title | Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group H32 at pH 7.5 | ||||||
![]() | Purine nucleoside phosphorylase deoD-type | ||||||
![]() | TRANSFERASE / Phosphorylase/hydrolase-like | ||||||
Function / homology | ![]() uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Santos, C.R. / Meza, A.N. / Martins, N.H. / Giuseppe, P.O. / Murakami, M.T. | ||||||
![]() | ![]() Title: Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases. Authors: de Giuseppe, P.O. / Martins, N.H. / Meza, A.N. / Dos Santos, C.R. / Pereira, H.D. / Murakami, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 457.4 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d8vC ![]() 4d8xC ![]() 4d8yC ![]() 4d9hC ![]() 4da0C ![]() 4da6C ![]() 4da7C ![]() 4da8C ![]() 4dabC ![]() 4daeC ![]() 4danC ![]() 4daoC ![]() 4darC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27562.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O34925, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THIS IS A CLONING ARTIFACT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES, 1%(v/v) MPD, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 47177 / % possible obs: 95.5 % / Redundancy: 8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.04 Å2 / Biso mean: 24.0276 Å2 / Biso min: 11.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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