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- PDB-5yaq: Crystal structure of scyllo-inositol dehydrogenase with L-glucose... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yaq | ||||||
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Title | Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with scyllo-inosose | ||||||
![]() | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | ||||||
![]() | OXIDOREDUCTASE / Rossman fold / homotetramer / sugar metabolism | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukano, K. / Shimizu, T. / Sasaki, Y. / Nakamura, A. / Yajima, S. | ||||||
![]() | ![]() Title: Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification Authors: Fukano, K. / Ozawa, K. / Kokubu, M. / Shimizu, T. / 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 | ![]() | 293.4 KB | Display | ![]() |
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PDB format | ![]() | 237 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 56.5 KB | Display | |
Data in CIF | ![]() | 78.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ya8C ![]() 5yabSC ![]() 5yapC 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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Unit cell |
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Components
#1: Protein | Mass: 41401.707 Da / Num. of mol.: 4 / Mutation: N72S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lgdA / Production host: ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.8 - 5.4, and 12 - 35% PEG3350 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 100761 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YAB Resolution: 1.99→39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.18 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.305 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→39 Å
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Refine LS restraints |
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