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- PDB-8b34: Structure of Human Aldose Reductase Mutant A299G with a Citrate M... -

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Basic information

Entry
Database: PDB / ID: 8b34
TitleStructure of Human Aldose Reductase Mutant A299G 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 A299G / transient pocket / nadp+ / diabetes / citrate
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 / metanephric collecting duct development / all-trans-retinol dehydrogenase (NADP+) activity / 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: 0.97 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 A299G with a Citrate Molecule Bound in the Anion Binding Pocket
Authors: Hubert, L.-S. / Heine, A. / Klebe, G.
History
DepositionSep 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 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)37,2374
Polymers36,1101
Non-polymers1,1283
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-2 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 66.845, 49.333
Angle α, β, γ (deg.)90.000, 91.897, 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: 36109.543 Da / Num. of mol.: 1 / Mutation: A299G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / Production host: Escherichia coli BL21 (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.: 488 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
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: 0.97→47.35 Å / Num. obs: 172687 / % possible obs: 95.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 6.43 Å2 / CC1/2: 0.998 / Rsym value: 0.05 / Net I/σ(I): 18
Reflection shellResolution: 0.97→1.03 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 26106 / CC1/2: 0.97 / Rsym value: 0.18 / % possible all: 89.2

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Processing

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

4prr


Resolution: 0.97→47.35 Å / SU ML: 0.0546 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.4126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.114 3454 2 %
Rwork0.1058 169232 -
obs0.1059 172686 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.3 Å2
Refinement stepCycle: LAST / Resolution: 0.97→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 74 488 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652894
X-RAY DIFFRACTIONf_angle_d1.07183982
X-RAY DIFFRACTIONf_chiral_restr0.0832438
X-RAY DIFFRACTIONf_plane_restr0.0083541
X-RAY DIFFRACTIONf_dihedral_angle_d17.67571109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.14211140.12685600X-RAY DIFFRACTION78.93
0.98-10.13991320.11316460X-RAY DIFFRACTION91.52
1-1.010.12211350.10496620X-RAY DIFFRACTION92.85
1.01-1.030.12651360.09826639X-RAY DIFFRACTION93.2
1.03-1.040.11471340.09316573X-RAY DIFFRACTION94.01
1.04-1.060.09631360.09426694X-RAY DIFFRACTION93.96
1.06-1.080.09261350.09046595X-RAY DIFFRACTION93.21
1.08-1.10.10381380.08356774X-RAY DIFFRACTION94.84
1.1-1.120.08551370.08226699X-RAY DIFFRACTION94.89
1.12-1.150.09541380.08026755X-RAY DIFFRACTION95.18
1.15-1.180.10431380.086778X-RAY DIFFRACTION95.35
1.18-1.210.10261380.08216767X-RAY DIFFRACTION95.29
1.21-1.240.08161370.08466723X-RAY DIFFRACTION94.84
1.24-1.270.10091400.08736824X-RAY DIFFRACTION96.32
1.27-1.320.11051400.08976891X-RAY DIFFRACTION96.66
1.32-1.360.10111410.09126894X-RAY DIFFRACTION96.98
1.36-1.420.10641410.09346890X-RAY DIFFRACTION97.27
1.42-1.480.10661390.09556832X-RAY DIFFRACTION95.6
1.48-1.560.12361420.09416947X-RAY DIFFRACTION98.05
1.56-1.660.11051420.0986994X-RAY DIFFRACTION98.21
1.66-1.790.11131440.10737012X-RAY DIFFRACTION98.5
1.79-1.970.11821430.1117038X-RAY DIFFRACTION98.45
1.97-2.250.11881420.11376950X-RAY DIFFRACTION97.38
2.25-2.830.13781460.1247145X-RAY DIFFRACTION99.66
2.83-47.350.11831460.1317138X-RAY DIFFRACTION98.43

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