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- PDB-8hnq: The structure of a alcohol dehydrogenase AKR13B2 with NADP -

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Basic information

Entry
Database: PDB / ID: 8hnq
TitleThe structure of a alcohol dehydrogenase AKR13B2 with NADP
ComponentsNADPH-dependent aldo/keto reductase AKR13B2
KeywordsTOXIN / dehydrogenase / DON / detoxification
Function / homology
Function and homology information


: / nucleotide binding / cytoplasm
Similarity search - Function
: / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / NADPH-dependent aldo/keto reductase AKR13B2
Similarity search - Component
Biological speciesDevosia sp. D6-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, M. / Yang, H. / Lu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The structure of AKR13B2
Authors: Chen, M. / Yang, H. / Lu, F.
History
DepositionDec 8, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-dependent aldo/keto reductase AKR13B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7205
Polymers31,3561
Non-polymers1,3644
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.114, 67.582, 87.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADPH-dependent aldo/keto reductase AKR13B2


Mass: 31355.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Devosia sp. D6-9 (bacteria) / Gene: AKR13B2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B8QJ47
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: evaporation / Details: PEG3350, TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→33.79 Å / Num. obs: 26019 / % possible obs: 95.84 % / Redundancy: 5.6 % / CC1/2: 0.993 / Net I/σ(I): 15.94
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 2555 / CC1/2: 0.947 / % possible all: 95.91

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.79 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 2000 7.69 %
Rwork0.1519 --
obs0.1545 26015 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 0 422 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082350
X-RAY DIFFRACTIONf_angle_d0.9893178
X-RAY DIFFRACTIONf_dihedral_angle_d15.727344
X-RAY DIFFRACTIONf_chiral_restr0.057339
X-RAY DIFFRACTIONf_plane_restr0.008410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24181340.17361701X-RAY DIFFRACTION96
2.05-2.110.23431450.15471676X-RAY DIFFRACTION96
2.11-2.170.1811380.15591695X-RAY DIFFRACTION96
2.17-2.240.20561450.1571701X-RAY DIFFRACTION96
2.24-2.320.21391320.15841686X-RAY DIFFRACTION96
2.32-2.410.24351410.16041681X-RAY DIFFRACTION95
2.41-2.520.19911430.15981733X-RAY DIFFRACTION98
2.52-2.650.21041490.15911724X-RAY DIFFRACTION97
2.65-2.820.21941470.16251734X-RAY DIFFRACTION98
2.82-3.040.18891420.16741735X-RAY DIFFRACTION98
3.04-3.340.19691450.15671736X-RAY DIFFRACTION96
3.34-3.830.15231440.13281733X-RAY DIFFRACTION96
3.83-4.820.13731460.12051743X-RAY DIFFRACTION95
4.82-33.790.15861490.16471737X-RAY DIFFRACTION91

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