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Yorodumi- PDB-3tjl: Crystal Structure of a Novel OYE from the Xylose-fermenting Fungu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tjl | ||||||
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Title | Crystal Structure of a Novel OYE from the Xylose-fermenting Fungus P. stipitis | ||||||
Components | NADPH dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Old yellow enzyme / Flavin mononucleotide / TIM barrel / NADPH oxidoreductase / Enone Reductase / Alkene reductase / stereocomplementarity / stereoselective / parallel alpha/beta barrel / biocatalysis / NADPH / FMN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Scheffersomyces stipitis CBS 6054 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Pompeu, Y.A. / Stewart, J.D. | ||||||
Citation | Journal: Adv.Synth.Catal. / Year: 2012 Title: Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions Authors: Pompeu, Y.A. / Sullivan, B. / Walton, A.Z. / 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 | 3tjl.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tjl.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tjl_validation.pdf.gz | 791.9 KB | Display | wwPDB validaton report |
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Full document | 3tjl_full_validation.pdf.gz | 793.4 KB | Display | |
Data in XML | 3tjl_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3tjl_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/3tjl ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tjl | HTTPS FTP |
-Related structure data
Related structure data | 3upwC 4df2C 1oyaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 45295.543 Da / Num. of mol.: 1 / Mutation: T169A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus) Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: OYE2.6, PICST_44614 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A3LT82, NADPH dehydrogenase | ||||
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#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | ChemComp-NA / #4: Chemical | #5: 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: 3.16 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M Sodium malonate 1-3% 2-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2011 / Details: Si 111 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→44 Å / Num. obs: 92358 / % possible obs: 0.996 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1OYA Resolution: 1.5→44 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 14.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.492 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→44 Å
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Refine LS restraints |
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LS refinement shell |
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