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Yorodumi- PDB-5lc1: L-threonine dehydrogenase from Trypanosoma brucei with NAD and th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lc1 | |||||||||
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Title | L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound. | |||||||||
Components | L-threonine 3-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase / holo-enzyme / Rossman fold | |||||||||
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: 2.1 Å | |||||||||
Authors | Erskine, P.T. / Adjogatse, E. / Wood, S.P. / 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 | 5lc1.cif.gz | 431.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lc1.ent.gz | 351.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/5lc1 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/5lc1 | HTTPS FTP |
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-Related structure data
Related structure data | 5k4qC 5k4tC 5k4uC 5k4vC 5k4wC 5k4yC 5k50C 5l9aSC 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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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 35847.305 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7YW97, L-threonine 3-dehydrogenase |
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-Non-polymers , 6 types, 1985 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-PYR / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / #7: 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: 2.2 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20 % w/v PEG 10K; TDH 2.0 mg/ml, 1 mM NAD(+), 30 mM pyruvate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.074 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→95.5 Å / Num. obs: 117204 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.2 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L9A Resolution: 2.1→95.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.668 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.176 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Note that the R-free set was chosen in thin resolution shells and hence the outer shell (Shell 1, below) did not contain any free-set ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Note that the R-free set was chosen in thin resolution shells and hence the outer shell (Shell 1, below) did not contain any free-set reflections. The R-free and N(R-free) given below relate the highest resolution shell which contained free-set reflections.
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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 mean: 22.767 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→95.5 Å
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Refine LS restraints |
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