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Yorodumi- PDB-3f03: Crystal structure of Pentaerythritol Tetranitrate Reductase compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f03 | ||||||
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Title | Crystal structure of Pentaerythritol Tetranitrate Reductase complex with 1-nitrocyclohexene | ||||||
Components | Pentaerythritol tetranitrate reductase | ||||||
Keywords | OXIDOREDUCTASE / Asymmetric hydrogenatio / bioreduction / biocatalysis / nitroalkenes / pentaerythritol tetranitrate reductase / stereo-control | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 Å | ||||||
Authors | Roujeinikova, A.R. / Toogood, H.S. / Leys, D. | ||||||
Citation | Journal: To be published Title: Structure-based insight into the asymmetric bioreduction of the C=C double bond of alpha,beta-unsaturated nitroalkenes by pentaerythritol tetranitrate reductase. Authors: Toogood, H.S. / Fryszkowska, A. / Hare, V. / Fisher, K. / Roujeinikova, A. / Leys, D. / Gardiner, J.M. / Stephens, G.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 | 3f03.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f03.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f03_validation.pdf.gz | 774.6 KB | Display | wwPDB validaton report |
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Full document | 3f03_full_validation.pdf.gz | 775.4 KB | Display | |
Data in XML | 3f03_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3f03_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f03 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f03 | HTTPS FTP |
-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
-Protein , 1 types, 1 molecules K
#1: Protein | Mass: 39404.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr / Plasmid: pONR1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, EC: 1.7.99.- |
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-Non-polymers , 5 types, 657 molecules
#2: Chemical | ChemComp-NYH / |
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#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-IPA / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | NYH AND IPA ARE IN ALTERNATE CONFORMATI |
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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: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 25 % (w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid pH 6.2, 17 % (v/v) isopropanol , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 8, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→44.432 Å / Num. obs: 112379 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.05 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.34→15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.259 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 / 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: 53.25 Å2 / Biso mean: 11.079 Å2 / Biso min: 3.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.375 Å / Total num. of bins used: 20
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