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Yorodumi- PDB-4hfm: X-ray Crystal Structure of a NADP(H)-bound Double Bond Reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hfm | ||||||
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Title | X-ray Crystal Structure of a NADP(H)-bound Double Bond Reductase from Nicotiana tabacum | ||||||
Components | Allyl alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / twisted b-barrel / Alkene reduction | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Toogood, H.S. / Scrutton, N.S. | ||||||
Citation | Journal: ACS Catal / Year: 2013 Title: Biocatalytic Asymmetric Alkene Reduction: Crystal Structure and Characterization of a Double Bond Reductase fromNicotiana tabacum. Authors: Mansell, D.J. / Toogood, H.S. / Waller, J. / Hughes, J.M. / Levy, C.W. / 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 | 4hfm.cif.gz | 270.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hfm.ent.gz | 219.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hfm_validation.pdf.gz | 1007 KB | Display | wwPDB validaton report |
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Full document | 4hfm_full_validation.pdf.gz | 1014.7 KB | Display | |
Data in XML | 4hfm_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 4hfm_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/4hfm ftp://data.pdbj.org/pub/pdb/validation_reports/hf/4hfm | HTTPS FTP |
-Related structure data
Related structure data | 4hfjC 4hfnC 3j3h 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: 39202.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: NtADH / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9SLN8, 2-alkenal reductase [NAD(P)+] #2: Chemical | #3: 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: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100mM KH2PO4/citrate buffer pH 4.5 + 45% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60.11 Å / Num. obs: 59835 / Redundancy: 5.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3J3H 3j3h Resolution: 1.9→57.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.478 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.134 / ESU R Free: 0.125 / 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 mean: 27.215 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→57.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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