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- PDB-7uei: Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uei | |||||||||
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Title | Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 100 K, 1.2 A, crystal 16 | |||||||||
![]() | Alcohol dehydrogenase E chain | |||||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase / horse liver / NAD / pentafluorobenzyl alcohol / 100 K | |||||||||
Function / homology | ![]() alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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. / Gakhar, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Dependence of crystallographic atomic displacement factors on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenases Authors: Plapp, B.V. / Gakhar, L. / Subramanian, R. #1: ![]() Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.8 KB | Display | ![]() |
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PDB format | ![]() | 282 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 59.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ua6C ![]() 7uc9C ![]() 7ucaC ![]() 7ucuC ![]() 7uddC ![]() 7udeC ![]() 7udrSC ![]() 7uecC ![]() 7ueeC ![]() 7uefC ![]() 7uejC ![]() 7uhvC ![]() 7uhwC ![]() 7uhxC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 842 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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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL Temp details: pH 6.7 at 298 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 cryostat / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2009 Details: ROSENBAUM ROCK VERTICAL FOCUSINGMIRROR WITH PT, GLASS, PD LANES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ROSENBAUM ROCK HIGH RESOLUTION DOUBLE CRYSTAL MONOCHROMATOR, LN2 COOLED, SAGITTAL FOCUSSING 2ND MIRROR, SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→20 Å / Num. obs: 219960 / % possible obs: 95.1 % / Redundancy: 4.05 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.03 / Rrim(I) all: 0.06 / Χ2: 1.14 / Net I/av σ(I): 8.8 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7udr Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.331 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.86 Å2 / Biso mean: 15.709 Å2 / Biso min: 7.62 Å2
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Refinement step | Cycle: final / Resolution: 1.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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