+Open data
-Basic information
Entry | Database: PDB / ID: 6f84 | ||||||
---|---|---|---|---|---|---|---|
Title | AKR1B1 at 2.55 MGy radiation dose. | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / oxidative stress / radiation damage / diabetes / non-genetic mutation | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Castellvi, A. / Juanhuix, J. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation. Authors: Castellvi, A. / Crespo, I. / Crosas, E. / Camara-Artigas, A. / Gavira, J.A. / Aranda, M.A.G. / Pares, X. / Farres, J. / Juanhuix, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f84.cif.gz | 162 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f84.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 6f84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/6f84 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/6f84 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6f7rC 6f81C 6f82C 6f8oC 2j8tS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase | ||
---|---|---|---|
#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 6000, AmCitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9017 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2017 |
Radiation | Monochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9017 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→49.51 Å / Num. obs: 127354 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.09→1.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 5997 / CC1/2: 0.892 / Rpim(I) all: 0.183 / Rrim(I) all: 0.341 / % possible all: 94.9 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2j8t Resolution: 1.09→10 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→10 Å
|