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Yorodumi- PDB-3wmw: GalE-like L-Threonine dehydrogenase from Cupriavidus necator (apo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wmw | ||||||
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Title | GalE-like L-Threonine dehydrogenase from Cupriavidus necator (apo form) | ||||||
Components | NAD dependent epimerase/dehydratase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / dehydrogenase / NAD+ binding | ||||||
Function / homology | Function and homology information Isomerases; Intramolecular oxidoreductases / isomerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Ralstonia eutropha (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Nakano, S. / Okazaki, S. / Tokiwa, H. / Asano, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase Authors: Nakano, S. / Okazaki, S. / Tokiwa, H. / Asano, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wmw.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wmw.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wmw_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 3wmw_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 3wmw_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 3wmw_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/3wmw ftp://data.pdbj.org/pub/pdb/validation_reports/wm/3wmw | HTTPS FTP |
-Related structure data
Related structure data | 3wmxC 3a4vS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 5 - 313 / Label seq-ID: 25 - 333
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-Components
#1: Protein | Mass: 38874.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_B0820, h16_B0820 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0K312, Oxidoreductases #2: Chemical | ChemComp-CA / #3: 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: 2.08 Å3/Da / Density % sol: 40.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20%(w/v) PEG3350, 0.2M Calcium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.8 Å / Num. obs: 31326 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A4V Resolution: 2.25→48.8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.534 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.233 / 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: 36.762 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→48.8 Å
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Refine LS restraints |
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