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Yorodumi- PDB-2b67: Crystal structure of the Nitroreductase Family Protein from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b67 | ||||||
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Title | Crystal structure of the Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4 | ||||||
Components | COG0778: Nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta sandwich / FMN binding pocket / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Kim, Y. / Volkart, L. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4 Authors: Kim, Y. / Volkart, L. / Abdullah, J. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b67.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b67.ent.gz | 155.4 KB | Display | PDB format |
PDBx/mmJSON format | 2b67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/2b67 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/2b67 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23129.896 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: Q97S03, UniProt: A0A0H2UP38*PLUS, NADH dehydrogenase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ACY / | #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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 8000, MES, Calcium Acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.02 Å / Num. all: 56901 / Num. obs: 54339 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5056 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→39.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.038 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.189 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→39.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.052→2.105 Å / Total num. of bins used: 20
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