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- PDB-7u25: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 7u25
TitleCrystal structure of arabidopsis thaliana acetohydroxyacid synthase W574L mutant in complex with bispyribac-sodium
ComponentsAcetolactate synthase, chloroplastic
KeywordsLIGASE / Herbicide / Resistance / AHAS / ALS
Function / homology
Function and homology information


acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / response to herbicide / chloroplast stroma / chloroplast / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6QL / FLAVIN-ADENINE DINUCLEOTIDE / Chem-TZD / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsGuddat, L.W. / Cheng, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of resistance to herbicides that target acetohydroxyacid synthase.
Authors: Lonhienne, T. / Cheng, Y. / Garcia, M.D. / Hu, S.H. / Low, Y.S. / Schenk, G. / Williams, C.M. / Guddat, L.W.
History
DepositionFeb 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4967
Polymers64,5131
Non-polymers1,9846
Water00
1
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,99314
Polymers129,0252
Non-polymers3,96812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area13280 Å2
ΔGint-137 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.952, 179.952, 185.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetolactate synthase, chloroplastic / AtALS / Acetohydroxy-acid synthase / Protein CHLORSULFURON RESISTANT 1


Mass: 64512.578 Da / Num. of mol.: 1 / Mutation: W574L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALS, AHAS, CSR1, TZP5, At3g48560, T8P19.70 / Production host: Escherichia coli (E. coli) / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 6 types, 6 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-6QL / 2,6-bis[(4,6-dimethoxypyrimidin-2-yl)oxy]benzoic acid


Mass: 430.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N4O8
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#6: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

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: 6.72 Å3/Da / Density % sol: 81.69 % / Description: Yellow diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: CHES buffer, potassium sodium tartrate, ammonium sulfate
PH range: 9.4-9.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.19→48.43 Å / Num. obs: 29873 / % possible obs: 99.4 % / Redundancy: 15.4 % / CC1/2: 0.998 / Net I/σ(I): 13.3
Reflection shellResolution: 3.19→3.39 Å / Num. unique obs: 4587 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2O

5k2o


Resolution: 3.19→48.43 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 1996 6.7 %
Rwork0.1735 27780 -
obs0.1748 29776 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.44 Å2 / Biso mean: 83.6366 Å2 / Biso min: 40.81 Å2
Refinement stepCycle: final / Resolution: 3.19→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 130 0 4568
Biso mean--77.67 --
Num. residues----582
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 (%)
3.19-3.270.35491260.32261786191290
3.27-3.360.27651400.281319402080100
3.36-3.460.27641420.253119672109100
3.46-3.570.2681390.228519392078100
3.57-3.70.23511420.212819792121100
3.7-3.850.25521410.191219622103100
3.85-4.020.19861420.177719762118100
4.02-4.230.18431420.162919722114100
4.23-4.50.16621440.137820042148100
4.5-4.850.15011420.138619832125100
4.85-5.330.17691450.149720062151100
5.33-6.10.17881460.167320232169100
6.1-7.680.19091470.166820632210100
7.69-48.430.15251580.15112180233899

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