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- PDB-7f7k: Crystal structure of AKR4C17 bound with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7f7k
TitleCrystal structure of AKR4C17 bound with NADP+
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / AKR4-2
Similarity search - Component
Biological speciesEchinochloa colona (jungle rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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)72,6189
Polymers70,6882
Non-polymers1,9307
Water4,666259
1
A: AKR4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2434
Polymers35,3441
Non-polymers8983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12890 Å2
MethodPISA
2
B: AKR4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3765
Polymers35,3441
Non-polymers1,0324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.671, 77.671, 454.088
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-581-

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-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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.36→25 Å / Num. obs: 34654 / % possible obs: 99.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.032 / Rrim(I) all: 0.094 / Χ2: 1.075 / Net I/σ(I): 6.6 / Num. measured all: 259466
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.447.70.42633420.8910.1530.4570.35398.9
2.44-2.547.80.34133510.9250.1210.3650.39499.4
2.54-2.667.80.26333850.940.0950.2820.45199.4
2.66-2.87.70.20334160.9670.0730.2180.56799.6
2.8-2.977.60.15134200.980.0550.1620.73899.6
2.97-3.27.50.12134310.9880.0440.130.96699.4
3.2-3.527.30.09734460.9910.0350.1041.43999
3.52-4.036.80.08934390.9930.0330.0962.04198.3
4.03-5.076.70.07735430.9930.030.0842.3598.7
5.07-258.10.04538810.9990.0160.0481.60699.2

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Processing

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

3h7u


Resolution: 2.36→24.89 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 1998 5.79 %
Rwork0.1883 32494 -
obs0.1906 34492 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.29 Å2 / Biso mean: 45.8649 Å2 / Biso min: 21.98 Å2
Refinement stepCycle: final / Resolution: 2.36→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 117 259 5252
Biso mean--57.42 46.02 -
Num. residues----619
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 (%)
2.36-2.420.27571380.22022233237198
2.42-2.490.26531370.22282240237799
2.49-2.560.23141390.211622522391100
2.56-2.640.28241410.21452286242799
2.64-2.740.28811390.214822892428100
2.74-2.840.24961410.21242281242299
2.84-2.970.24611430.200423062449100
2.97-3.130.24731400.21692296243699
3.13-3.330.26061410.2012301244299
3.33-3.580.23581420.19262311245399
3.58-3.940.22611440.16922335247998
3.94-4.510.18111450.15492352249798
4.51-5.670.18751480.17052407255599
5.67-24.890.21191600.18632605276599

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