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- PDB-5y1f: Monomeric L-threonine 3-dehydrogenase from metagenome database (N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y1f | ||||||
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Title | Monomeric L-threonine 3-dehydrogenase from metagenome database (NAD+ bound form) | ||||||
![]() | NAD dependent epimerase/dehydratase family | ||||||
![]() | OXIDOREDUCTASE / dehydrogenase / NAD+ | ||||||
Function / homology | ![]() L-threonine 3-dehydrogenase activity / threonine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Motoyama, T. / Nakano, S. / Yamamoto, Y. / Tokiwa, H. / Asano, Y. / Ito, S. | ||||||
![]() | ![]() Title: Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase. Authors: Motoyama, T. / Nakano, S. / Yamamoto, Y. / Tokiwa, H. / Asano, Y. / Ito, 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 | ![]() | 91.3 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743.6 KB | Display | ![]() |
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Full document | ![]() | 749.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y1dC ![]() 5y1eC ![]() 5y1gC ![]() 3wmxS 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: 37542.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2M Sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→54.9 Å / Num. obs: 75876 / % possible obs: 91.5 % / Redundancy: 6.3 % / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.25→1.28 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WMX Resolution: 1.25→54.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.656 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / 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: 14.098 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→54.89 Å
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Refine LS restraints |
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