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- PDB-2wsb: Crystal structure of the short-chain dehydrogenase Galactitol- De... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wsb | ||||||
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Title | Crystal structure of the short-chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD | ||||||
![]() | GALACTITOL DEHYDROGENASE | ||||||
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Function / homology | ![]() galactitol 2-dehydrogenase (L-tagatose-forming) / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carius, Y. / Christian, H. / Faust, A. / Kornberger, P. / Kohring, G.W. / Giffhorn, F. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Structural Insight Into Substrate Differentiation of the Sugar-Metabolizing Enzyme Galactitol Dehydrogenase from Rhodobacter Sphaeroides D. Authors: Carius, Y. / Christian, H. / Faust, A. / Zander, U. / Klink, B.U. / Kornberger, P. / Kohring, G.W. / Giffhorn, F. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.5 KB | Display | ![]() |
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PDB format | ![]() | 404.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 26408.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NAD / ![]() #4: Chemical | ChemComp-POL / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 Details: 4% N-PROPANOLE, 100MM SODIUM CACODYLATE, PH 6.5, 200MM SODIUM ACETATE, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→19.94 Å / Num. obs: 313700 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: SWISS PROT MODEL Resolution: 1.25→19.94 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.548 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.041 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→19.94 Å
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Refine LS restraints |
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