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- PDB-2is7: Crystal Structure of Aldose Reductase complexed with Dichlorophen... -

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Basic information

Entry
Database: PDB / ID: 2is7
TitleCrystal Structure of Aldose Reductase complexed with Dichlorophenylacetic acid
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / TIM-Barrel / ARI / aldo-keto reductase
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. / 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
(2,6-DICHLOROPHENYL)ACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHarrison, D.H.T. / Milne, A. / Brownlee, J.M.
CitationJournal: Bioorg.Chem. / Year: 2006
Title: Structural and thermodynamic studies of simple aldose reductase-inhibitor complexes.
Authors: Brownlee, J.M. / Carlson, E. / Milne, A.C. / Pape, E. / Harrison, D.H.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,7173
Polymers35,7681
Non-polymers9482
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.990, 67.146, 92.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase


Mass: 35768.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-2CL / (2,6-DICHLOROPHENYL)ACETIC ACID


Mass: 205.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 % PEG 6000, 50 mM Citrate, subsequent glutaraldehyde x-link, ligand soak, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 20, 1998 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 41729 / Num. obs: 30223 / % possible obs: 72.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.13 % / Rmerge(I) obs: 0.087 / Χ2: 8.708 / Net I/σ(I): 26.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 1.11 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.55 / Num. unique all: 358 / Χ2: 1.804 / % possible all: 17.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1AZ1

1az1


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.017 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1434 5.1 %RANDOM
Rwork0.169 ---
obs0.17 28352 81.38 %-
all-34840 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 60 107 2683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222642
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9953598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3165314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.27424.825114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1681511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021969
X-RAY DIFFRACTIONr_nbd_refined0.1980.21154
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.25
X-RAY DIFFRACTIONr_mcbond_it0.881.51629
X-RAY DIFFRACTIONr_mcangle_it1.40122568
X-RAY DIFFRACTIONr_scbond_it2.22931174
X-RAY DIFFRACTIONr_scangle_it3.4964.51030
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 65 -
Rwork0.207 1254 -
obs-1319 51.75 %

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