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Yorodumi- PDB-5k4y: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k4y | ||||||
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Title | Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei refined to 1.77 angstroms | ||||||
Components | L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Short-chain dehydrogenase / threonine / holo | ||||||
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: 1.77 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 | 5k4y.cif.gz | 426.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k4y.ent.gz | 350.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/5k4y ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k4y | HTTPS FTP |
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-Related structure data
Related structure data | 5k4qC 5k4tC 5k4uC 5k4vC 5k4wC 5k50C 5l9aC 5lc1C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#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 |
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-Non-polymers , 6 types, 1475 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-GOL / | #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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M tri-sodium citrate, 25% w/v PEG 4K, 0.2M sodium acetate, NAD+ (10mM) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92001 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.77→40.12 Å / Num. obs: 203411 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→39.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.129 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107
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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: 85.03 Å2 / Biso mean: 19.218 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: final / Resolution: 1.77→39.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.774→1.82 Å / Total num. of bins used: 20
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