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- PDB-6f84: AKR1B1 at 2.55 MGy radiation dose. -

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Basic information

Entry
Database: PDB / ID: 6f84
TitleAKR1B1 at 2.55 MGy radiation dose.
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / 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 / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / metanephric collecting duct development / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / retinoid metabolic process / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsCastellvi, A. / Juanhuix, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Consejo de Seguridad Nuclear Spain
CitationJournal: 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
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0264
Polymers35,8981
Non-polymers1,1283
Water5,873326
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-3 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.378, 66.730, 49.539
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 6000, AmCitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9017 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2017
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9017 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j8t

2j8t


Resolution: 1.09→10 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1516 --
Rwork0.1201 --
obs-127186 99.3 %
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 1.09→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 74 294 2871

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