[English] 日本語
Yorodumi- PDB-4dao: Crystal structure of the hexameric purine nucleoside phosphorylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dao | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with adenine | ||||||
Components | Purine nucleoside phosphorylase deoD-type | ||||||
Keywords | TRANSFERASE / Phosphorylase/hydrolase-like | ||||||
Function / homology | Function and homology information purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å | ||||||
Authors | Giuseppe, P.O. / Martins, N.H. / Meza, A.N. / Murakami, M.T. | ||||||
Citation | Journal: Plos One / Year: 2012 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dao.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dao.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/4dao ftp://data.pdbj.org/pub/pdb/validation_reports/da/4dao | HTTPS FTP |
---|
-Related structure data
Related structure data | 4d8vC 4d8xC 4d8yC 4d98C 4d9hC 4da0C 4da6C 4da7C 4da8C 4dabC 4daeC 4danC 4darC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27562.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU19630, deoD, punB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: O34925, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THIS IS A CLONING ARTIFACT | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 4.6 Details: 0.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 twin |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.22→40 Å / Num. obs: 29480 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.044 / Χ2: 1.005 / Net I/σ(I): 18.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2067 / WRfactor Rwork: 0.1443 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8508 / SU B: 7.099 / SU ML: 0.15 / SU R Cruickshank DPI: 0.0365 / SU Rfree: 0.0357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 71.61 Å2 / Biso mean: 40.3613 Å2 / Biso min: 20.43 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.22→2.277 Å / Total num. of bins used: 20
|