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Yorodumi- PDB-4yil: OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)AC... -
+Open data
-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 | ||||||
Components | NADPH dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / CATALYTIC ACTIVITY / FMN BINDING | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / NADPH dehydrogenase activity / FMN binding Similarity search - Function | ||||||
Biological species | Saccharomyces pastorianus (lager yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 Å | ||||||
Authors | Santangelo, S. / Brenna, E. / Stewart, J.D. / Powell III, R.W. | ||||||
Citation | Journal: Adv.Synth.Catal. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yil.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yil.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/4yil ftp://data.pdbj.org/pub/pdb/validation_reports/yi/4yil | HTTPS FTP |
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-Related structure data
Related structure data | 4yncC 4gbuS S: Starting model for refinement 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
-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.) Saccharomyces pastorianus (lager yeast) Gene: OYE1 / Plasmid: pET3b / Details (production host): pSA01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02899, NADPH dehydrogenase |
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-Non-polymers , 5 types, 487 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.95 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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