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Yorodumi- PDB-5k4w: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k4w | ||||||
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Title | Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NADH and L-threonine refined to 1.72 angstroms | ||||||
Components | L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Short-chain dehydrogenase / threonine / holo / ligand-bound | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Adjogatse, E.A. / Erskine, P.T. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Authors: Adjogatse, E. / Erskine, P. / Wells, S.A. / Kelly, J.M. / Wilden, J.D. / Chan, A.W.E. / Selwood, D. / Coker, A. / Wood, S. / 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 | 5k4w.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k4w.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 5k4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/5k4w ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k4w | HTTPS FTP |
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-Related structure data
Related structure data | 5k4qC 5k4tC 5k4uC 5k4vC 5k4yC 5k50C 5l9aC 5lc1C 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
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 35847.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7YW97, L-threonine 3-dehydrogenase |
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-Non-polymers , 5 types, 429 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M sodium acetate, 0.1M Tris, 30% w/v PEG 4000, NADH (10mM), L-Threonine (30mM) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.72→46.32 Å / Num. obs: 67909 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→43.14 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.97 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.102
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.69 Å2 / Biso mean: 27.667 Å2 / Biso min: 13.07 Å2
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Refinement step | Cycle: final / Resolution: 1.72→43.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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