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- PDB-8hw0: the structure of AKR6D1 -

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Basic information

Entry
Database: PDB / ID: 8hw0
Titlethe structure of AKR6D1
ComponentsNADPH-dependent aldo/keto reductase AKR6D1
KeywordsTOXIN / dehydrogenase
Function / homologyPotassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / oxidoreductase activity / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH-dependent aldo/keto reductase AKR6D1
Function and homology information
Biological speciesDevosia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChen, M. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structure of AKR6D1
Authors: Chen, M. / Yang, H. / Lv, F.
History
DepositionDec 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent aldo/keto reductase AKR6D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6234
Polymers36,6951
Non-polymers9283
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.650, 157.650, 111.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-946-

HOH

31A-988-

HOH

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Components

#1: Protein NADPH-dependent aldo/keto reductase AKR6D1


Mass: 36695.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Devosia (bacteria) / Gene: AKR6D1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B8QIS5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 4.71 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 293 K / Method: evaporation / Details: NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→19.85 Å / Num. obs: 110879 / % possible obs: 99.93 % / Redundancy: 26.3 % / CC1/2: 0.999 / Net I/σ(I): 25.84
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 10918 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIXV3.0refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.85 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 2000 1.8 %
Rwork0.1748 --
obs0.1749 110872 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 60 493 3129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092696
X-RAY DIFFRACTIONf_angle_d1.3013660
X-RAY DIFFRACTIONf_dihedral_angle_d15.481368
X-RAY DIFFRACTIONf_chiral_restr0.059394
X-RAY DIFFRACTIONf_plane_restr0.006466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.20421400.2257660X-RAY DIFFRACTION100
1.54-1.580.20191420.20837698X-RAY DIFFRACTION100
1.58-1.630.22931410.20987680X-RAY DIFFRACTION100
1.63-1.680.22081420.20237720X-RAY DIFFRACTION100
1.68-1.740.22521420.2017721X-RAY DIFFRACTION100
1.74-1.810.19461420.19327728X-RAY DIFFRACTION100
1.81-1.890.2131420.19617742X-RAY DIFFRACTION100
1.89-1.990.19511420.19247737X-RAY DIFFRACTION100
1.99-2.110.20441430.18457763X-RAY DIFFRACTION100
2.11-2.280.20921420.18057765X-RAY DIFFRACTION100
2.28-2.510.18131430.18067791X-RAY DIFFRACTION100
2.51-2.870.17311440.17737839X-RAY DIFFRACTION100
2.87-3.610.1711460.15897868X-RAY DIFFRACTION100
3.61-19.850.14051490.14898160X-RAY DIFFRACTION100

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