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- PDB-7f7m: AKR4C17 in complex with NADP+ and glyphosate -

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Basic information

Entry
Database: PDB / ID: 7f7m
TitleAKR4C17 in complex with NADP+ and glyphosate
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
GLYPHOSATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / AKR4-2
Similarity search - Component
Biological speciesEchinochloa colona (jungle rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,5377
Polymers70,6882
Non-polymers1,8495
Water3,117173
1
A: AKR4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2583
Polymers35,3441
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12990 Å2
MethodPISA
2
B: AKR4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2804
Polymers35,3441
Non-polymers9363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.640, 77.640, 451.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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-GPJ / GLYPHOSATE


Mass: 170.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO5P / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
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: 1.00797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00797 Å / Relative weight: 1
ReflectionResolution: 2.47→25 Å / Num. obs: 29709 / % possible obs: 97.3 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.122 / Χ2: 1.202 / Net I/σ(I): 5.6 / Num. measured all: 254457
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.47-2.568.50.49128910.8640.1520.5180.39498.7
2.56-2.668.90.42429590.8730.1320.4470.47399.8
2.66-2.789.10.33929910.9330.1050.3570.5599.8
2.78-2.939.20.25929170.9550.0810.2740.74399.1
2.93-3.119.10.20429920.970.0650.2161.01899.1
3.11-3.358.70.16129640.9820.0530.1711.38198.5
3.35-3.698.30.12729330.9870.0430.1351.76996.7
3.69-4.227.80.10528820.9890.0370.1122.07393.9
4.22-5.317.60.09229520.9910.0320.0982.29494
5.31-258.30.06332280.9970.0210.0671.68194.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7U

3h7u


Resolution: 2.47→24.82 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1998 6.76 %
Rwork0.1944 27542 -
obs0.1978 29540 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.09 Å2 / Biso mean: 50.0085 Å2 / Biso min: 21.19 Å2
Refinement stepCycle: final / Resolution: 2.47→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 116 173 5157
Biso mean--60.2 46.35 -
Num. residues----618
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 (%)
2.47-2.530.32761380.21811906204497
2.53-2.60.31431430.231919792122100
2.6-2.680.30731420.227119582100100
2.68-2.760.28741420.229519552097100
2.76-2.860.27561440.233319842128100
2.86-2.980.31341430.23391964210799
2.98-3.110.31431430.23831979212299
3.11-3.270.2641420.22221955209799
3.27-3.480.25061410.20481947208897
3.48-3.750.23651410.18731946208796
3.75-4.120.22261400.16041931207195
4.12-4.710.26611390.15761911205093
4.72-5.930.17611460.17582013215995
5.93-24.820.20021540.192114226892

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