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- PDB-8h2a: Crystal structure of alcohol dehydrogenase from Formosa agariphila -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h2a | ||||||
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Title | Crystal structure of alcohol dehydrogenase from Formosa agariphila | ||||||
![]() | Alcohol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Alcohol dehydrogenase | ||||||
Function / homology | ![]() alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brott, S. / Bornscheuer, U.T. / Nam, K.H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of alcohol dehydrogenase from Formosa agariphila Authors: Brott, S. / Bornscheuer, U.T. / Nam, K.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 547 KB | Display | ![]() |
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PDB format | ![]() | 452.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 8 MB | Display | ![]() |
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Full document | ![]() | 8.2 MB | Display | |
Data in XML | ![]() | 117.5 KB | Display | |
Data in CIF | ![]() | 153.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ljhS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39490.020 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 15362 / KCTC 12365 / LMG 23005 / KMM 3901 / M-2Alg 35-1 Gene: BN863_21030 / Production host: ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, pH 7.5, KCl and PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 98086 / % possible obs: 97.5 % / Redundancy: 5.7 % / CC1/2: 0.976 / Net I/σ(I): 12.78 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 4819 / CC1/2: 0.751 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LJH Resolution: 2.5→48.19 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.52 Å2 / Biso mean: 51.1087 Å2 / Biso min: 18.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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