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- PDB-7w1x: Crystal structure of AKR4C16 bound with NADPH -

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Basic information

Entry
Database: PDB / ID: 7w1x
TitleCrystal structure of AKR4C16 bound with NADPH
ComponentsAKR4-1
KeywordsOXIDOREDUCTASE / Glyphosate resistance / GPJ degradation mechanism / aldo-keto reductase / structure-based engineering
Function / homology
Function and homology information


aldose reductase (NADPH) activity / nucleotide binding / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 Science Foundation (NSF, China)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
DepositionNov 21, 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: AKR4-1
B: AKR4-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1034
Polymers70,6122
Non-polymers1,4912
Water9,368520
1
A: AKR4-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0522
Polymers35,3061
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area12690 Å2
MethodPISA
2
B: AKR4-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0522
Polymers35,3061
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.716, 81.782, 68.741
Angle α, β, γ (deg.)90.000, 104.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AKR4-1


Mass: 35306.082 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: A0A5J6VMF4
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 297 K / Method: evaporation / Details: 30 % PEG 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.9→34.88 Å / Num. obs: 42954 / % possible obs: 99.9 % / Redundancy: 6.96 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0987 / Net I/σ(I): 11.58
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.4476 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 1965

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Processing

Software
NameVersionClassification
SAINTdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h7u

3h7u


Resolution: 1.9→34.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.498 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 2159 5 %RANDOM
Rwork0.2006 ---
obs0.2036 40721 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.6 Å2 / Biso mean: 24.845 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.48 Å2
2--0.71 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 1.9→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 96 520 5469
Biso mean--22.48 30.95 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174661
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.6426949
X-RAY DIFFRACTIONr_angle_other_deg1.2421.57910857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.435616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.252246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44715839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6931523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 150 -
Rwork0.291 3017 -
all-3167 -
obs--99.84 %

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