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- PDB-2r24: Human Aldose Reductase structure -

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Basic information

Entry
Database: PDB / ID: 2r24
TitleHuman Aldose Reductase structure
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / beta/alpha-8 TIM barrel / Cataract / NADP
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
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
IDD594 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsBlakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O.N. / Cousido-Siah, A. ...Blakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O.N. / Cousido-Siah, A. / Haertlein, M. / Joachimiak, A. / Myles, D. / Podjarny, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Quantum model of catalysis based on mobile proton revealed by subatomic X-Ray and neutron diffraction studies of h-Aldose Reductase
Authors: Blakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O.N. / Cousido-Siah, A. / Haertlein, M. / Joachimiak, A. / Myles, D. / Podjarny, A.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Data collection
Revision 1.3Mar 14, 2012Group: Database references / Structure summary
Revision 1.4Apr 25, 2018Group: Data collection / Category: diffrn_source
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)37,0583
Polymers35,8981
Non-polymers1,1602
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.066, 67.126, 47.862
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / / AR / Aldehyde reductase


Mass: 35898.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-LDT / IDD594 / [2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)-5-FLUORO-PHENOXY]-ACETIC ACID


Mass: 416.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12BrF2NO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-ID1
NUCLEAR REACTORILL LADI2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2LAUELneutron1
1x-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→40.11 Å / Num. obs: 46319 / Biso Wilson estimate: 17.52 Å2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
AMoREphasing
Refinement

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureResolution (Å)Refine-IDBaniso 11 (Å2)Baniso 12 (Å2)Baniso 13 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDIsotropic thermal modelσ(F)Phase errorBsol (Å2)ksol (e/Å3)
MOLECULAR REPLACEMENT1.752-33.563X-RAY DIFFRACTION5.337800.43095.45604.24070.1660.12860.1322952315249.3698.780.191Isotropic1.3315.3929.3920.347
2.194-40.11NEUTRON DIFFRACTION-0.7034-0-1.2513-6.6254-0-7.07190.29120.25660.2596992118848.3572.790.4521.5326.9282.9040.53
Refinement stepCycle: LAST / Resolution: 1.752→33.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 72 285 2882
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0185216
NEUTRON DIFFRACTIONf_angle_d1.7599458
NEUTRON DIFFRACTIONf_dihedral_angle_d25.11363
NEUTRON DIFFRACTIONf_chiral_restr0.16392
NEUTRON DIFFRACTIONf_plane_restr0.011779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.752-1.78090.25691330.20531080X-RAY DIFFRACTION79.23
1.7809-1.81160.22151580.16781321X-RAY DIFFRACTION99.46
1.8116-1.84450.22031720.15591344X-RAY DIFFRACTION99.61
1.8445-1.880.1821410.14141371X-RAY DIFFRACTION99.6
1.88-1.91840.21171420.13771380X-RAY DIFFRACTION99.54
1.9184-1.96010.19211360.12981340X-RAY DIFFRACTION99.8
1.9601-2.00570.16051440.1221386X-RAY DIFFRACTION99.48
2.0057-2.05580.15941430.11921353X-RAY DIFFRACTION99.8
2.0558-2.11140.16961710.1131337X-RAY DIFFRACTION99.74
2.1114-2.17350.15531430.11861377X-RAY DIFFRACTION99.8
2.1735-2.24370.18731230.12061368X-RAY DIFFRACTION100
2.2437-2.32380.17551420.12591385X-RAY DIFFRACTION99.87
2.3238-2.41680.15431300.12311381X-RAY DIFFRACTION99.8
2.4168-2.52680.15721370.12381394X-RAY DIFFRACTION100
2.5268-2.660.17961620.12181351X-RAY DIFFRACTION100
2.66-2.82650.1651310.12781384X-RAY DIFFRACTION100
2.8265-3.04470.16911380.11981385X-RAY DIFFRACTION100
3.0447-3.35080.13731220.11751413X-RAY DIFFRACTION100
3.3508-3.83510.12461290.1051378X-RAY DIFFRACTION99.87
3.8351-4.82950.11361250.10351420X-RAY DIFFRACTION99.68
4.8295-33.5630.17981300.14091424X-RAY DIFFRACTION99.36
2.194-2.30980.3632980.32321196NEUTRON DIFFRACTION56.09
2.3098-2.45450.33641170.30951269NEUTRON DIFFRACTION59.97
2.4545-2.6440.33511330.28771350NEUTRON DIFFRACTION63.92
2.644-2.910.30751410.26711475NEUTRON DIFFRACTION69.69
2.91-3.33090.30821520.25711669NEUTRON DIFFRACTION77.65
3.3309-4.19590.25351750.2111915NEUTRON DIFFRACTION88.97
4.1959-40.110.20591760.19782018NEUTRON DIFFRACTION92.61

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