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Yorodumi- PDB-2j3k: Crystal structure of Arabidopsis thaliana Double Bond Reductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j3k | ||||||
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Title | Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary Complex II | ||||||
Components | NADPH-dependent oxidoreductase 2-alkenal reductase | ||||||
Keywords | OXIDOREDUCTASE / ARABIDOPSIS THALIANA / 4-HYDROXY-2- NONENAL / NADP / TERNARY COMPLEX II / DOUBLE BOND REDUCTASE (AT5G16970) | ||||||
Function / homology | Function and homology information 2-alkenal reductase [NAD(P)+] / 2-alkenal reductase [NAD(P)+] activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / plastid / response to oxidative stress / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Youn, B. / Kim, S.J. / Moinuddin, S.G. / Lee, C. / Bedgar, D.L. / Harper, A.R. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 Title: Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970. Authors: Youn, B. / Kim, S.J. / Moinuddin, S.G. / Lee, C. / Bedgar, D.L. / Harper, A.R. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j3k.cif.gz | 150.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j3k.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3k ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3k | HTTPS FTP |
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-Related 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: 38175.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 References: UniProt: Q39172, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, 2-alkenal reductase [NAD(P)+] #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: reservoir solution containing 20% (w/v) polyethylene glycol 3350 and 0.2 M potassium chloride Temp details: 277 and 293 K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07812 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07812 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 23815 / % possible obs: 82.6 % / Observed criterion σ(I): 2 / Redundancy: 5.38 % / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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