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- PDB-8y4b: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8y4b | ||||||
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Title | Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to L-2,4-DKDF and NADH | ||||||
![]() | SDR family oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / dehydrogenase / Rossmann Fold | ||||||
Function / homology | : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Akagashi, M. / Watanabe, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a alpha-furanosyl hemiketal of substrates. Authors: Akagashi, M. / Watanabe, S. / Kwiatkowski, S. / Drozak, J. / Terawaki, S. / Watanabe, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 42.4 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xwkC ![]() 8y11C ![]() 8y46C ![]() 8y4jC C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27596.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-A1LXB / | Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION #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: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.2 M Sodium acetate, 0.1 M Tris-HCl pH8.5, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→44.32 Å / Num. obs: 110122 / % possible obs: 100 % / Redundancy: 19.57 % / CC1/2: 0.991 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.67→1.7 Å / Num. unique obs: 5406 / CC1/2: 0.759 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold Resolution: 1.67→44.32 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→44.32 Å
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Refine LS restraints |
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LS refinement shell |
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