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Yorodumi- PDB-3uko: Crystal Structure of S-Nitrosoglutathione Reductase from Arabidop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uko | ||||||
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Title | Crystal Structure of S-Nitrosoglutathione Reductase from Arabidopsis thaliana, complex with NADH | ||||||
Components | Alcohol dehydrogenase class-3 | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase III / homodimer / reduction of GSNO / NADH binding | ||||||
Function / homology | Function and homology information S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Weichsel, A. / Crotty, J. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Crystal structure and kinetic behavior of alcohol dehydrogenase III /S-nitrosoglutathione reductase from arabidopsis thaliana Authors: Crotty, J. / Greving, M. / Brettschneider, S. / Weichsel, A. / Wildner, G.F. / Vierling, E. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uko.cif.gz | 342.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uko.ent.gz | 281 KB | Display | PDB format |
PDBx/mmJSON format | 3uko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/3uko ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3uko | HTTPS FTP |
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-Related structure data
Related structure data | 1m6hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40615.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH2, ADHIII, FDH1, At5g43940, MRH10.4 / Plasmid: pJC20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96533, alcohol dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, S-(hydroxymethyl)glutathione dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / #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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.1 M ammonium sulfate, 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006 / Details: bent Si-mirror |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39 Å / Num. all: 166757 / Num. obs: 166757 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.8 / Num. unique all: 16554 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M6H Resolution: 1.4→38.92 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.645 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.841 Å2
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Refine analyze | Luzzati coordinate error obs: 0.228 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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