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- PDB-4yil: OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)AC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yil | ||||||
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Title | OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)ACRYLATE IN A NON PRODUCTIVE BINDING MODE | ||||||
![]() | NADPH dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / CATALYTIC ACTIVITY / FMN BINDING | ||||||
Function / homology | ![]() NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Santangelo, S. / Brenna, E. / Stewart, J.D. / Powell III, R.W. | ||||||
![]() | ![]() Title: Opposite Enantioselectivity in the Bioreduction of (Z)-beta-Aryl-beta-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R)- and (S)-beta-Aryl-gamma-lactams Authors: Brenna, E. / Crotti, M. / Gatti, F.G. / Monti, D. / Parmeggiani, F. / Powell III, R.W. / Santangelo, S. / 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 | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.9 KB | Display | ![]() |
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Full document | ![]() | 784 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yncC ![]() 4gbuS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44566.953 Da / Num. of mol.: 1 / Mutation: W116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: OYE1 / Plasmid: pET3b / Details (production host): pSA01 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 487 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/4D3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/4D3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMN / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-4D3 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 0.2M MgCl2, 0.1M Na HEPES, 35% PEG 400, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.461→32.52 Å / Num. all: 74409 / Num. obs: 74409 / % possible obs: 98.46 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.29 |
Reflection shell | Resolution: 1.461→1.491 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 4.38 / % possible all: 97.19 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GBU Resolution: 1.461→32.521 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.39 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.21 Å2 / Biso mean: 21.8773 Å2 / Biso min: 12.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.461→32.521 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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