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Open data
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Basic information
Entry | Database: PDB / ID: 5ela | ||||||
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Title | The structure of DHAR1 from Arabidopsis thaliana | ||||||
![]() | Glutathione S-transferase DHAR1, mitochondrial | ||||||
![]() | TRANSFERASE / Dehydroascobate reductase / glutathione S-transferase / Arabidopsis thaliana / CLIC / Chloride ion channel | ||||||
Function / homology | ![]() response to symbiotic fungus / regulation of biological process involved in symbiotic interaction / acquisition of seed longevity / positive regulation of salicylic acid mediated signaling pathway / protein glutathionylation / ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / response to jasmonic acid ...response to symbiotic fungus / regulation of biological process involved in symbiotic interaction / acquisition of seed longevity / positive regulation of salicylic acid mediated signaling pathway / protein glutathionylation / ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / response to jasmonic acid / response to ozone / plant-type vacuole / apoplast / monoatomic ion channel complex / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / monoatomic ion transmembrane transport / chloroplast / defense response / cellular response to hydrogen peroxide / peroxisome / copper ion binding / mitochondrion / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Menault, M. / Roszak, A.W. / Lapthorn, A.J. | ||||||
![]() | ![]() Title: Arabidopsis thaliana DHAR1 apo structure Authors: Menault, M. / Roszak, A.W. / Lapthorn, A.J. #1: Journal: J. Biol. Chem. / Year: 2002 Title: Functional divergence in the glutathione transferase superfamily in plants. Identification of two classes with putative functions in redox homeostasis in Arabidopsis thaliana. Authors: Dixon, D.P. / Davis, B.G. / Edwards, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.8 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 440.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5el8SC ![]() 5elgC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24776.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9FWR4, glutathione transferase, glutathione dehydrogenase (ascorbate) |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.45 % / Description: hexagonal bipyramidal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein at 20 mg/ml, 20% PEG 8000, 0.2 M NaK Phosphate, 0.1M TRIS PH range: 7.0 -8 .5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014 |
Radiation | Monochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→54.01 Å / Num. obs: 15525 / % possible obs: 99.7 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 2.28→2.34 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 5.1 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EL8 Resolution: 2.28→54.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 11.546 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2022 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.18 / SU Rfree Cruickshank DPI: 0.1798 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.144 Å2
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Refinement step | Cycle: 1 / Resolution: 2.28→54.01 Å
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Refine LS restraints |
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