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- PDB-4ng5: V203A horse liver alcohol dehydrogenase E complexed with NAD+ and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ng5 | ||||||
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Title | V203A horse liver alcohol dehydrogenase E complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / dehydrogenase / NAD / liver cytosol | ||||||
Function / homology | ![]() : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Plapp, B.V. | ||||||
![]() | ![]() Title: Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Authors: Yahashiri, A. / Rubach, J.K. / 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 | ![]() | 350.6 KB | Display | ![]() |
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PDB format | ![]() | 285.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nfhC ![]() 4nfsC ![]() 4dwvS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: 39825.223 Da / Num. of mol.: 2 / Mutation: V203A Source method: isolated from a genetically manipulated source Details: tac promoter / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1064 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 | ChemComp-MRD / ( #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2- ...Details: 50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 Details: ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS DOUBLE CRYSTAL CRYOCOOLED SI(111) |
Radiation | Monochromator: DOUBLE CRYSTAL CRYOCOOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. all: 261399 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.25 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.8 / Num. unique all: 16455 / % possible all: 54.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DWV Resolution: 1.1→17.91 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.702 / SU ML: 0.015 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.529 Å2
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Refine analyze | Luzzati coordinate error free: 0.026 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→17.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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