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Yorodumi- PDB-6jyg: Crystal Structure of L-threonine dehydrogenase from Phytophthora ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jyg | ||||||
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Title | Crystal Structure of L-threonine dehydrogenase from Phytophthora infestans | ||||||
Components | L-threonine 3-dehydrogenase, putative | ||||||
Keywords | OXIDOREDUCTASE / L-threonine dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phytophthora infestans (potato late blight agent) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Yoneda, K. / Sakuraba, H. / Ohshima, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Enzyme.Microb.Technol. / Year: 2020 Title: Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans. Authors: Yoneda, K. / Nagano, R. / Mikami, T. / Sakuraba, H. / Fukui, K. / Araki, T. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jyg.cif.gz | 379 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jyg.ent.gz | 309 KB | Display | PDB format |
PDBx/mmJSON format | 6jyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jyg_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6jyg_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6jyg_validation.xml.gz | 82.1 KB | Display | |
Data in CIF | 6jyg_validation.cif.gz | 106.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jyg ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jyg | HTTPS FTP |
-Related structure data
Related structure data | 3a1nS 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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-Components
#1: Protein | Mass: 38304.457 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora infestans (strain T30-4) (eukaryote) Strain: T30-4 / Gene: PITG_05140 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: D0N3N0 #2: Chemical | ChemComp-FLC / #3: Chemical | #4: Chemical | ChemComp-NAD / #5: 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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 40 % PEG600 0.1 M Citrate buffer (pH 5.8) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 107201 / % possible obs: 93.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.31→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.451 / Num. unique obs: 5137 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A1N Resolution: 2.31→49.28 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 40.3 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→49.28 Å
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LS refinement shell | Resolution: 2.31→2.45 Å
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