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- PDB-8aqg: Structure of Human Aldose Reductase Mutant A299G/L300G with a Cit... -

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Basic information

Entry
Database: PDB / ID: 8aqg
TitleStructure of Human Aldose Reductase Mutant A299G/L300G with a Citrate Molecule Bound in the Anion Binding Pocket
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / mutant A299/L300G / nadp+ / diabetes
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. / 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
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: 0.95 Å
AuthorsHubert, L.-S. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Human Aldose Reductase Mutant A299/L300G with a Citrate Molecule Bound in the Anion Binding Pocket
Authors: Hubert, L.-S. / Heine, A. / Klebe, G.
History
DepositionAug 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5504
Polymers35,4231
Non-polymers1,1283
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-3 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.427, 66.762, 49.388
Angle α, β, γ (deg.)90.000, 92.021, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 35422.809 Da / Num. of mol.: 1 / Mutation: A299G, L300G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET 15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, 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.: 444 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→47.4 Å / Num. obs: 187163 / % possible obs: 96.8 % / Redundancy: 3.87 % / Biso Wilson estimate: 6.1 Å2 / CC1/2: 1 / Rsym value: 0.02 / Net I/σ(I): 29.29
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 6.1 / Num. unique obs: 27066 / CC1/2: 0.97 / Rsym value: 0.16 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRR

4prr


Resolution: 0.95→38.65 Å / SU ML: 0.0499 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.6406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1162 3744 2 %
Rwork0.1095 183406 -
obs0.1096 187150 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.82 Å2
Refinement stepCycle: LAST / Resolution: 0.95→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 74 444 2988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622853
X-RAY DIFFRACTIONf_angle_d1.0533927
X-RAY DIFFRACTIONf_chiral_restr0.0814424
X-RAY DIFFRACTIONf_plane_restr0.0081537
X-RAY DIFFRACTIONf_dihedral_angle_d17.84911102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.14021010.13734919X-RAY DIFFRACTION70.6
0.96-0.970.12381180.12845786X-RAY DIFFRACTION82.85
0.97-0.990.14221330.11516498X-RAY DIFFRACTION91.8
0.99-10.11851380.10756760X-RAY DIFFRACTION97.76
1-1.020.11171390.10156830X-RAY DIFFRACTION97.62
1.02-1.030.11171400.09786865X-RAY DIFFRACTION98.01
1.03-1.050.09281420.09226938X-RAY DIFFRACTION98.51
1.05-1.070.10021390.09126832X-RAY DIFFRACTION98.2
1.07-1.090.0971400.08676865X-RAY DIFFRACTION98.15
1.09-1.110.0881430.0846986X-RAY DIFFRACTION99.07
1.11-1.130.08571410.08386908X-RAY DIFFRACTION98.99
1.13-1.150.11141420.08466955X-RAY DIFFRACTION98.9
1.15-1.180.10711410.08486919X-RAY DIFFRACTION98.95
1.18-1.210.09241400.08736870X-RAY DIFFRACTION98.33
1.21-1.240.10871420.08836940X-RAY DIFFRACTION98.69
1.24-1.280.09551410.09176948X-RAY DIFFRACTION99.01
1.28-1.320.10471420.09516956X-RAY DIFFRACTION99.09
1.32-1.370.11071420.09396925X-RAY DIFFRACTION98.99
1.37-1.420.10871410.09856929X-RAY DIFFRACTION98.83
1.42-1.490.10411410.09916902X-RAY DIFFRACTION98.09
1.49-1.570.11841420.10016979X-RAY DIFFRACTION99.52
1.57-1.670.11081430.10346988X-RAY DIFFRACTION99.43
1.67-1.790.11091420.11086957X-RAY DIFFRACTION99.04
1.79-1.970.11291420.11876969X-RAY DIFFRACTION98.44
1.97-2.260.12721420.12096933X-RAY DIFFRACTION98.37
2.26-2.850.14811420.1316977X-RAY DIFFRACTION98.9
2.85-38.650.12731450.13377072X-RAY DIFFRACTION98.61

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