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Yorodumi- PDB-3lba: The Crystal Structure of smu.1229 from Streptococcus mutans UA159... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lba | ||||||
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Title | The Crystal Structure of smu.1229 from Streptococcus mutans UA159 bound to hypoxanthine | ||||||
Components | Putative purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / punA / Glycosyltransferase | ||||||
Function / homology | Function and homology information nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Su, X.-D. / Hou, Q.M. / Wang, H.F. / Liu, X. | ||||||
Citation | Journal: TO BE PUBLISHED Title: The Crystal Structure of smu.1229 from Streptococcus mutans UA159 bound to hypoxanthine Authors: Su, X.-D. / Hou, Q.M. / Wang, H.F. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lba.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lba.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/3lba ftp://data.pdbj.org/pub/pdb/validation_reports/lb/3lba | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32431.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.1229 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8DTU4, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-HPA / |
#3: Chemical | ChemComp-SO4 / |
#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: 53.43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 0.15M ammonium sulfate, 0.1M bis-tris, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→63 Å / Num. all: 15986 / Num. obs: 15986 / % possible obs: 100 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.6 Å2 |
Reflection shell | Resolution: 2.24→2.36 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→34.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.908 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.205 / 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: 67.1 Å2 / Biso mean: 34.225 Å2 / Biso min: 13.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→34.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.298 Å / Total num. of bins used: 20
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Xplor file |
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