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Yorodumi- PDB-3gfb: L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic arch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gfb | ||||||
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Title | L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis | ||||||
Components | L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Cytoplasm / Metal-binding / NAD / Zinc | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / L-threonine catabolic process to glycine / threonine metabolic process / amino acid binding / NAD+ binding / protein homotetramerization / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bowyer, A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis Authors: Bowyer, A. / Mikolajek, H. / Stuart, J.W. / Wood, S.P. / Jamil, F. / Rashid, N. / Akhtar, M. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gfb.cif.gz | 289.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gfb.ent.gz | 235.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/3gfb ftp://data.pdbj.org/pub/pdb/validation_reports/gf/3gfb | HTTPS FTP |
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-Related structure data
Related structure data | 2dfvS S: Starting model for refinement |
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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: 38147.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: tdh, TK0916 / Plasmid: pET-8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q5JI69, L-threonine 3-dehydrogenase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.05 M sodium citrate, 2.4 M ammonium sulfate, 0.1 M sodium/potassium tartrate, 5%(v/v) glycerol and 0.1 mM zinc chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 12, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→73.92 Å / Num. obs: 84056 / % possible obs: 100 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.146 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9511 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2DFV Resolution: 2.4→73.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.937 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.255 / 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: 38.704 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→73.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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