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Yorodumi- PDB-3p8i: Y351F mutant of pentaerythritol tetranitrate reductase containing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p8i | ||||||
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Title | Y351F mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule | ||||||
Components | Pentaerythritol tetranitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / old yellow enzyme family / alpha / beta barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 Å | ||||||
Authors | Toogood, H.S. / Scrutton, N.S. | ||||||
Citation | Journal: Catalysis Science and Technology / Year: 2011 Title: Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions ...Title: Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions with a,b-unsaturated nitroolefins Authors: Fryszkowska, A. / Toogood, H.S. / Sakuma, M. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p8i.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p8i.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 3p8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/3p8i ftp://data.pdbj.org/pub/pdb/validation_reports/p8/3p8i | HTTPS FTP |
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-Related structure data
Related structure data | 3p84C 3p8jC 1h50S C: citing same article (ref.) S: Starting model for refinement |
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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: 39519.199 Da / Num. of mol.: 1 / Mutation: Y351F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr, PETNR / Plasmid: pBluescript II-KS(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, NADPH dehydrogenase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-ACT / |
#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: 2.19 Å3/Da / Density % sol: 43.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 22, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→37.4 Å / Num. all: 111179 / Num. obs: 111179 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.19→1.23 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H50 Resolution: 1.19→7.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1452 / WRfactor Rwork: 0.1276 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9359 / SU B: 0.936 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0352 / SU Rfree: 0.0331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.46 Å2 / Biso mean: 13.1949 Å2 / Biso min: 4.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→7.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.22 Å / Total num. of bins used: 20
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