[English] 日本語
Yorodumi- PDB-5k4q: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k4q | ||||||
---|---|---|---|---|---|---|---|
Title | Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ refined to 2.3 angstroms | ||||||
Components | L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase / ligand-bound / holo | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / threonine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Adjogatse, E.K. / Cooper, J.B. / Erskine, P.T. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5k4q.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k4q.ent.gz | 328.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k4q_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5k4q_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5k4q_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 5k4q_validation.cif.gz | 109.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/5k4q ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k4q | HTTPS FTP |
-Related structure data
Related structure data | 5k4tC 5k4uC 5k4vC 5k4wC 5k4yC 5k50C 5l9aC 5lc1C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35709.160 Da / Num. of mol.: 6 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 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M lithium sulphate, 0.1M Tris, 30% w/v PEG 4K, pH 8.5, NAD+ (0.09mM) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Feb 3, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→48.143 Å / Num. obs: 93173 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.143 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.84 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.245
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.91 Å2 / Biso mean: 21.09 Å2 / Biso min: 2 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→48.143 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|