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- PDB-7f7j: The crystal structure of AKR4C17 -

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Basic information

Entry
Database: PDB / ID: 7f7j
TitleThe crystal structure of AKR4C17
ComponentsAKR4-2
KeywordsOXIDOREDUCTASE / Glyphosate resistance / GPJ degradation mechanism / aldo-keto reductase / structure-based engineering
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 4C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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
Similarity search - Domain/homology
Biological speciesEchinochloa colona (jungle rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLi, H. / Yang, Y. / Hu, Y. / Chen, C.-C. / Huang, J.-W. / Min, J. / Dai, L. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFC2100300 China
CitationJournal: J Hazard Mater / Year: 2022
Title: Structural analysis and engineering of aldo-keto reductase from glyphosate-resistant Echinochloa colona
Authors: Li, H. / Yang, Y. / Hu, Y. / Chen, C.C. / Huang, J.W. / Min, J. / Dai, L. / Guo, R.T.
History
DepositionJun 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AKR4-2
B: AKR4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8434
Polymers70,6882
Non-polymers1552
Water11,854658
1
B: AKR4-2
hetero molecules

A: AKR4-2


Theoretical massNumber of molelcules
Total (without water)70,8434
Polymers70,6882
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area940 Å2
ΔGint-31 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.612, 77.612, 451.986
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

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Components

#1: Protein AKR4-2


Mass: 35344.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinochloa colona (jungle rice) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5J6VLZ7
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 2.0 M Ammonium sulfate, 0.1 M MES pH 6.5 and 0.01 M CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.93→25 Å / Num. obs: 59007 / % possible obs: 94.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.042 / Rrim(I) all: 0.126 / Χ2: 2.358 / Net I/σ(I): 7.9 / Num. measured all: 458237
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-28.50.32654660.9510.1030.3430.81990.3
2-2.088.30.26555270.9620.0840.281.09991.2
2.08-2.178.20.22755880.9750.0720.2391.41891.4
2.17-2.297.50.21556030.9750.0710.2281.78491.5
2.29-2.437.80.18357360.9780.060.1941.95993.2
2.43-2.627.50.16258300.9820.0550.1722.29295
2.62-2.887.10.13960160.9860.050.1492.71196.7
2.88-3.36.80.11461760.990.0440.1233.25898.7
3.3-4.156.60.09762380.9930.0390.1053.99797.8
4.15-259.40.08868270.9950.0310.0933.90699.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7U

3h7u


Resolution: 1.93→24.82 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1999 3.4 %
Rwork0.1802 56779 -
obs0.1812 58778 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.32 Å2 / Biso mean: 24.9985 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.93→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 6 658 5439
Biso mean--47.91 32.23 -
Num. residues----607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.980.27261310.2133747387889
1.98-2.030.22031340.1793801393591
2.03-2.090.19781360.17653823395991
2.09-2.160.2221340.17823847398191
2.16-2.240.24071360.19023854399092
2.24-2.330.26581350.20713840397591
2.33-2.430.22981410.18433997413894
2.43-2.560.19941400.18123986412695
2.56-2.720.23181440.19454099424396
2.72-2.930.19581480.19394181432997
2.93-3.230.24691500.1854276442699
3.23-3.690.20391500.17584269441998
3.69-4.640.17871540.15074368452299
4.65-24.820.19361660.18244691485798

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