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Yorodumi- PDB-4k8e: OYE1-W116V complexed with the aromatic product of (R)-carvone dis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k8e | ||||||
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Title | OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation | ||||||
Components | NADPH dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / Old Yellow Enzyme / carvone / TIM-barrel / NADPH dehydrogenase 1 | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces pastorianus (lager yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 Å | ||||||
Authors | Sullivan, B. / Pompeu, Y.A. / Stewart, J.D. | ||||||
Citation | Journal: ACS CATALYSIS / Year: 2013 Title: X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase Authors: Pompeu, Y.A. / Sullivan, B. / Stewart, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k8e.cif.gz | 317.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k8e.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k8e_validation.pdf.gz | 818.1 KB | Display | wwPDB validaton report |
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Full document | 4k8e_full_validation.pdf.gz | 818.2 KB | Display | |
Data in XML | 4k8e_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 4k8e_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k8e ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k8e | HTTPS FTP |
-Related structure data
Related structure data | 3txzC 4gbuC 4ge8C 4gweC 4gxmC 4h6kC 4k7vC 4k7yC 4k8hC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44984.562 Da / Num. of mol.: 1 / Mutation: W116V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces pastorianus (lager yeast) Gene: OYE1 / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q02899, NADPH dehydrogenase |
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-Non-polymers , 8 types, 657 molecules
#2: Chemical | ChemComp-FMN / | ||||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-0WV / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-PGE / #9: 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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3 , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 15, 2011 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.269→24.2088 Å / Num. obs: 113545 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.59 |
Reflection shell | Resolution: 1.27→1.32 Å / Redundancy: 9 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.47 / Num. unique all: 11082 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.269→24.204 Å / SU ML: 0.1 / σ(F): 1.37 / Phase error: 9.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.269→24.204 Å
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Refine LS restraints |
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LS refinement shell |
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