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Yorodumi- PDB-5y1g: Monomeric L-threonine 3-dehydrogenase from metagenome database (A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y1g | ||||||
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Title | Monomeric L-threonine 3-dehydrogenase from metagenome database (AKB and NADH bound form) | ||||||
Components | NAD dependent epimerase/dehydratase family | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / 2-amino 3-ketobutyrate / NADH | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase activity / threonine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | uncultured archaeon MedDCM-OCT-S05-C57 (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Motoyama, T. / Nakano, S. / Yamamoto, Y. / Tokiwa, H. / Asano, Y. / Ito, S. | ||||||
Citation | Journal: Biochemistry / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y1g.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y1g.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 5y1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y1g_validation.pdf.gz | 761.3 KB | Display | wwPDB validaton report |
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Full document | 5y1g_full_validation.pdf.gz | 766 KB | Display | |
Data in XML | 5y1g_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 5y1g_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/5y1g ftp://data.pdbj.org/pub/pdb/validation_reports/y1/5y1g | HTTPS FTP |
-Related structure data
Related structure data | 5y1dC 5y1eC 5y1fC 3wmxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) uncultured archaeon MedDCM-OCT-S05-C57 (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: D6PBM7 |
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#2: Chemical | ChemComp-AKB / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.97 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→54.3 Å / Num. obs: 64955 / % possible obs: 99.7 % / Redundancy: 6.6 % / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.35→1.38 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMX Resolution: 1.35→54.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.69 / 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: 12.321 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→54.32 Å
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Refine LS restraints |
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