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- PDB-3oq6: Horse liver alcohol dehydrogenase A317C mutant complexed with NAD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oq6 | ||||||
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Title | Horse liver alcohol dehydrogenase A317C mutant complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
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Function / homology | ![]() alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Plapp, B.V. / Herdendorf, T.J. | ||||||
![]() | ![]() Title: Origins of the high catalytic activity of human alcohol dehydrogenase 4 studied with horse liver A317C alcohol dehydrogenase. Authors: Herdendorf, T.J. / Plapp, B.V. #1: ![]() Title: Structures of horse liver alcohol dehydrogenase complexed with NAD and substituted benzyl alcohols Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.6 KB | Display | ![]() |
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PDB format | ![]() | 283.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1hldS S: Starting model for refinement |
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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, 2 molecules AB
#1: Protein | Mass: 39885.336 Da / Num. of mol.: 2 / Mutation: A317C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1109 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/PFB.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/PFB.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ![]() #4: Chemical | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow![]() | Temperature: 298 K / Method: microdialysis / pH: 7 Details: 50 mM ammonium TES [N-tris(hydroxymethyl)-2-aminoethane sulfonate], 25% MRD, 11 mg/ml protein, 11 mM NAD+, 5 mM 2,3,4,5,6-pentafluorobenzyl alcohol, pH 7.0, MICRODIALYSIS, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 27, 2009 / Details: SAGGITALLY FOCUSED MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→90 Å / Num. obs: 214213 / % possible obs: 92.2 % / Redundancy: 3.57 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1 / Net I/σ(I): 9.4 / Scaling rejects: 5787 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1hld Resolution: 1.2→19.85 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1442 / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8668 / SU B: 1.303 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0359 / SU Rfree: 0.0362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. B107 GLU O TOO CLOSE TO B741 O, BECAUSE OF A WOBBLE IN THE PEPTIDE BACKBONE THAT THE AUTHORS ARE UNABLE TO FIT PROPERLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.31 Å2 / Biso mean: 17.5778 Å2 / Biso min: 5.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.229 Å / Total num. of bins used: 20
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