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Open data
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Basic information
Entry | Database: PDB / ID: 4k8h | ||||||
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Title | OYE1-W116V complexed with (R)-carvone | ||||||
![]() | NADPH dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / Old Yellow Enzyme / carvone / TIM-barrel / NADPH dehydrogenase 1 | ||||||
Function / homology | ![]() NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sullivan, B. / Pompeu, Y.A. / Stewart, J.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.8 KB | Display | ![]() |
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PDB format | ![]() | 205.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.6 KB | Display | ![]() |
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Full document | ![]() | 809.9 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3txzC ![]() 4gbuC ![]() 4ge8C ![]() 4gweC ![]() 4gxmC ![]() 4h6kC ![]() 4k7vC ![]() 4k7yC ![]() 4k8eC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: OYE1 / Plasmid: pET3b / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 550 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/07V.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/07V.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMN / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-07V / ( | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-1PE / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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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: ![]() ![]() ![]() |
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: 1.55→35.4862 Å / Num. obs: 63649 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3.8 / Num. unique all: 6275 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.55→35.477 Å
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Refine LS restraints |
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LS refinement shell |
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