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Yorodumi- PDB-3s2s: The crystal structure of pyrazinamidase/nicotinamidase from strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s2s | ||||||
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Title | The crystal structure of pyrazinamidase/nicotinamidase from streptococcus mutans UA159 | ||||||
Components | Putative pyrazinamidase/nicotinamidase | ||||||
Keywords | HYDROLASE / pyrazinamidase/nicotinamidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Su, X.-D. / Liu, X. / Zhang, H. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer Authors: Liu, X. / Zhang, H. / Wang, X.J. / Li, L.F. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s2s.cif.gz | 318.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s2s.ent.gz | 259.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/3s2s ftp://data.pdbj.org/pub/pdb/validation_reports/s2/3s2s | HTTPS FTP |
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-Related 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: 24091.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pncA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DSG2, nicotinamidase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20%(v/v) MPD, 0.1M Sodium Cacodylylate trihydrate(pH 4.5) , 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-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 205235 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 22.52 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.977 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8977 / SU ML: 0.17 / σ(F): 2 / Phase error: 16.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.912 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.51 Å2 / Biso mean: 29.0305 Å2 / Biso min: 9.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.977 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 57.4739 Å / Origin y: 37.4782 Å / Origin z: 82.6439 Å
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Refinement TLS group |
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