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- PDB-4xzn: Crystal structure of the methylated K125R/V301L AKR1B10 Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 4xzn
TitleCrystal structure of the methylated K125R/V301L AKR1B10 Holoenzyme
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / TIM barrel / Aldo-keto reductase 1B10 / Holoenzyme / Cytosolic
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / extracellular region / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Podjarny, A.
CitationJournal: Chemmedchem / Year: 2015
Title: Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10.
Authors: Ruiz, F.X. / Cousido-Siah, A. / Porte, S. / Dominguez, M. / Crespo, I. / Rechlin, C. / Mitschler, A. / de Lera, A.R. / Martin, M.J. / de la Fuente, J.A. / Klebe, G. / Pares, X. / Farres, J. / Podjarny, A.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 10, 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
X: Aldo-keto reductase family 1 member B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2533
Polymers36,4471
Non-polymers8052
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-1 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.914, 79.914, 50.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Aldo-keto reductase family 1 member B10 / ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase ...ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase / SI reductase


Mass: 36447.121 Da / Num. of mol.: 1 / Mutation: K125R, V301L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Production host: Escherichia coli (E. coli)
References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% PEG 6000, 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91907 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 37876 / % possible obs: 93.9 % / Redundancy: 3.4 % / Rsym value: 0.068 / Net I/σ(I): 14.51
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.36 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUA

1zua


Resolution: 1.7→34.604 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 1893 5 %Random 5%
Rwork0.1955 ---
obs0.1971 37861 93.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 52 180 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082791
X-RAY DIFFRACTIONf_angle_d1.43799
X-RAY DIFFRACTIONf_dihedral_angle_d16.0861074
X-RAY DIFFRACTIONf_chiral_restr0.08410
X-RAY DIFFRACTIONf_plane_restr0.008478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6923-1.73470.28841270.23322575X-RAY DIFFRACTION94
1.7347-1.78160.29691430.24592572X-RAY DIFFRACTION95
1.7816-1.8340.31011250.23412581X-RAY DIFFRACTION95
1.834-1.89320.28271340.22192635X-RAY DIFFRACTION95
1.8932-1.96080.25491520.22462576X-RAY DIFFRACTION96
1.9608-2.03930.26661290.21752617X-RAY DIFFRACTION96
2.0393-2.13210.25921330.20522603X-RAY DIFFRACTION95
2.1321-2.24450.24081250.19472618X-RAY DIFFRACTION96
2.2445-2.38510.21881460.20472638X-RAY DIFFRACTION96
2.3851-2.56920.21681390.19842617X-RAY DIFFRACTION96
2.5692-2.82770.25591420.20042598X-RAY DIFFRACTION95
2.8277-3.23660.20391390.19482586X-RAY DIFFRACTION95
3.2366-4.07670.21081390.17692526X-RAY DIFFRACTION92
4.0767-34.6110.20651200.18082226X-RAY DIFFRACTION81

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