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- PDB-4d8y: Crystal structure of the hexameric purine nucleoside phosphorylas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d8y | ||||||
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Title | Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group P212121 at pH 5.6 | ||||||
![]() | Purine nucleoside phosphorylase deoD-type | ||||||
![]() | TRANSFERASE / Phosphorylase/hydrolase-like | ||||||
Function / homology | ![]() purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / 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 | ![]() | 307.4 KB | Display | ![]() |
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PDB format | ![]() | 251 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4d8vC ![]() 4d8xC ![]() 4d98C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 27562.137 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O34925, purine-nucleoside phosphorylase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: 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: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.6 Details: 0.1 M sodium citrate, 2 M ammonium sulfate, 0.2 M sodium potassium tartrate, pH 5.6, 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: 1.61→50 Å / Num. obs: 235074 / % possible obs: 98.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 62.14 Å2 / Biso mean: 22.806 Å2 / Biso min: 8.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.651 Å / Total num. of bins used: 20
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