+Open data
-Basic information
Entry | Database: PDB / ID: 3h7r | ||||||
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Title | Crystal structure of the plant stress-response enzyme AKR4C8 | ||||||
Components | Aldo-keto reductase | ||||||
Keywords | OXIDOREDUCTASE / stress response / aldo-keto reductase / NADP / drought tolerance | ||||||
Function / homology | Function and homology information steroid dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / : / response to water deprivation / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / aldose reductase (NADPH) activity / NADP+ binding / response to cadmium ion / response to salt stress ...steroid dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / : / response to water deprivation / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / aldose reductase (NADPH) activity / NADP+ binding / response to cadmium ion / response to salt stress / response to cold / response to toxic substance / oxidoreductase activity / endoplasmic reticulum / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | White, S.A. / Simpson, P.J. / Ride, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress. Authors: Simpson, P.J. / Tantitadapitak, C. / Reed, A.M. / Mather, O.C. / Bunce, C.M. / White, S.A. / Ride, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h7r.cif.gz | 153.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7r.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7r ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7r | HTTPS FTP |
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-Related structure data
Related structure data | 3h7uSC S: Starting model for refinement C: citing same article (ref.) |
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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: 36901.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g37760, DQ837653 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O80944 | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 200 mM Ammonium acetate, 50 mM Tri-sodium citrate dihydrate pH 6.0, 5% v/v Ethylene glycol, 32% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29.24 Å / Num. all: 63103 / Num. obs: 62514 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9158 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H7U Resolution: 1.4→28.24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.932 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.198 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→28.24 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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Refinement TLS params. | Method: refined / Origin x: 60.878 Å / Origin y: -0.029 Å / Origin z: 17.734 Å
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