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- PDB-6ktk: Crystal structure of scyllo-inositol dehydrogenase R178A mutant, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ktk | ||||||
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Title | Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from Paracoccus laeviglucosivorans | ||||||
![]() | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, M. / Koubara, K. / Takenoya, M. / Fukano, K. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans. Authors: Suzuki, M. / Koubara, K. / Takenoya, M. / Fukano, K. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, 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 | ![]() | 306.4 KB | Display | ![]() |
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PDB format | ![]() | 246.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ktjC ![]() 6ktlC ![]() 5yabS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 41315.594 Da / Num. of mol.: 4 / Mutation: R178A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lgdA / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-NAI / ![]() #3: Chemical | ![]() #4: Sugar | ChemComp-8S0 / #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | Sequence details | unintended mutation | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, pH 5.2, and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.65→50 Å / Num. obs: 190486 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 13395 / CC1/2: 0.898 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5yab Resolution: 1.65→48.4 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.65→48.4 Å
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LS refinement shell | Resolution: 1.65→1.69 Å
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