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- PDB-4xzm: Crystal structure of the methylated wild-type AKR1B10 holoenzyme -

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Basic information

Entry
Database: PDB / ID: 4xzm
TitleCrystal structure of the methylated wild-type AKR1B10 holoenzyme
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / TIM barrel / Aldo-Keto Reductase / 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 (NAD+) activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / mitochondrion / 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: 1.75 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)37,2243
Polymers36,4181
Non-polymers8052
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-1 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.435, 79.435, 49.796
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: 36418.098 Da / Num. of mol.: 1
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.: 178 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
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: 0.9202 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 35411 / % possible obs: 99 % / Redundancy: 3.2 % / Rsym value: 0.065 / Net I/σ(I): 16.64
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.97 / % possible all: 100

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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: 1.75→34.396 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 25.61 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1751 4.91 %Random 5%
Rwork0.203 ---
obs0.2054 35411 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→34.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 52 178 2801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082755
X-RAY DIFFRACTIONf_angle_d1.2663748
X-RAY DIFFRACTIONf_dihedral_angle_d15.0451063
X-RAY DIFFRACTIONf_chiral_restr0.077405
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.7940.28791460.28672615X-RAY DIFFRACTION95
1.794-1.84640.27121540.28672633X-RAY DIFFRACTION94
1.8464-1.90560.30641020.28052568X-RAY DIFFRACTION96
1.9056-1.97320.26151460.25482550X-RAY DIFFRACTION95
1.9732-2.05160.25511480.25642606X-RAY DIFFRACTION95
2.0516-2.1440.25831300.24932603X-RAY DIFFRACTION95
2.144-2.25580.23951160.23542613X-RAY DIFFRACTION96
2.2558-2.39530.25711450.24042569X-RAY DIFFRACTION95
2.3953-2.57720.29341300.24362571X-RAY DIFFRACTION95
2.5772-2.83110.26411640.22722610X-RAY DIFFRACTION94
2.8311-3.22840.26861160.20392593X-RAY DIFFRACTION96
3.2284-4.0220.23321130.1582599X-RAY DIFFRACTION96
4.022-9.92950.22411410.15012571X-RAY DIFFRACTION94

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