+Open data
-Basic information
Entry | Database: PDB / ID: 7bn7 | ||||||
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Title | Crystal structure of ene-reductase OYE2 from S. cerevisiae | ||||||
Components | OYE2 isoform 1 | ||||||
Keywords | OXIDOREDUCTASE / NADPH dehydrogenase | ||||||
Function / homology | FLAVIN MONONUCLEOTIDE / : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Robescu, M.S. / Bergantino, E. / Hall, M. / Cendron, L. | ||||||
Citation | Journal: Acs Catalysis / Year: 2022 Title: Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C=C Bond Isomerization Reaction Authors: Robescu, M.S. / Cendron, L. / Bacchin, A. / Wagner, K. / Reiter, T. / Janicki, I. / Merusic, K. / Illek, M. / Aleotti, M. / Bergantino, E. / Hall, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bn7.cif.gz | 353.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bn7.ent.gz | 262.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bn7_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7bn7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7bn7_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 7bn7_validation.cif.gz | 78.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bn7 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bn7 | HTTPS FTP |
-Related structure data
Related structure data | 7blfC 7bn6C 7bo0C 1oyaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45066.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OYE2, GI526_G0002963 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5PXJ0, NADPH dehydrogenase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 8 % w/v PEG 20,000/ 0.1 M Sodium acetate pH 4.5 0.25 M Potassium bromide 8 % v/v PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→49.19 Å / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 42.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.1 / Num. measured all: 394986 |
Reflection shell | Resolution: 2.45→2.538 Å / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26082 / CC1/2: 0.738 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1oya Resolution: 2.45→49.19 Å / SU ML: 0.3143 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5727 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→49.19 Å
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Refine LS restraints |
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LS refinement shell |
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