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Yorodumi- PDB-4dar: Crystal structure of the hexameric purine nucleoside phosphorylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dar | ||||||
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Title | Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with tubercidin | ||||||
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: 3.15 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dar.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dar.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/4dar ftp://data.pdbj.org/pub/pdb/validation_reports/da/4dar | HTTPS FTP |
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-Related structure data
Related structure data | 4d8vC 4d8xC 4d8yC 4d98C 4d9hC 4da0C 4da6C 4da7C 4da8C 4dabC 4daeC 4danC 4daoC C: citing same article (ref.) |
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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
#1: Protein | Mass: 27562.137 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-TBN / ' |
Sequence details | AUTHORS STATE THAT THIS IS A CLONING ARTIFACT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | Resolution: 3.15→117.466 Å / Num. all: 5743 / Num. obs: 5743 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rsym value: 0.116 / Net I/σ(I): 10.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.2818 / WRfactor Rwork: 0.2241 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8007 / SU B: 50.416 / SU ML: 0.402 / SU Rfree: 0.4967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 87.58 Å2 / Biso mean: 60.804 Å2 / Biso min: 41.33 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.23 Å / Total num. of bins used: 20
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