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Yorodumi- PDB-6tq5: Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tq5 | ||||||
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Title | Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): complex with NADP+ | ||||||
Components | Enzyme subunit | ||||||
Keywords | OXIDOREDUCTASE / Alcohol dehydrogenase / thermal stability / protein engineering | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Function and homology information | ||||||
Biological species | Starmerella magnoliae (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rovida, S. / Aalbers, F.S. / Fraaije, M.W. / Mattevi, A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Elife / Year: 2020 Title: Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering. Authors: Aalbers, F.S. / Furst, M.J. / Rovida, S. / Trajkovic, M. / Gomez Castellanos, J.R. / Bartsch, S. / Vogel, A. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tq5.cif.gz | 389.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tq5.ent.gz | 320 KB | Display | PDB format |
PDBx/mmJSON format | 6tq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/6tq5 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/6tq5 | HTTPS FTP |
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-Related structure data
Related structure data | 6tq3SC 6tq8C 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
#1: Protein | Mass: 25673.166 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Starmerella magnoliae (fungus) / Variant: DSMZ 70638 / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 20% w/v PEG 3350, 0.2 M sodium citrate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97264 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97264 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→84 Å / Num. obs: 134154 / % possible obs: 97.4 % / Redundancy: 3.6 % / CC1/2: 0.982 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.104 / Rrim(I) all: 0.2 / Net I/σ(I): 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TQ3 Resolution: 1.6→83.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.72 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.08 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES - REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.38 Å2 / Biso mean: 18.356 Å2 / Biso min: 7.26 Å2
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Refinement step | Cycle: final / Resolution: 1.6→83.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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