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- PDB-7u1u: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 7u1u
TitleCrystal structure of arabidopsis thaliana acetohydroxyacid synthase W574L mutant
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-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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 22, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)66,0576
Polymers64,5191
Non-polymers1,5395
Water00
1
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,11412
Polymers129,0372
Non-polymers3,07710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area12340 Å2
ΔGint-152 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.953, 177.953, 184.727
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: 64518.609 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 , 5 types, 5 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: 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
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4

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Details

Has ligand of interestN
Has protein modificationY

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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: 6.54 Å3/Da / Density % sol: 81.2 % / Description: Yellow diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: CHES buffer, potassium sodium tartrate, sodium 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: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.22→48.1 Å / Num. obs: 28382 / % possible obs: 99.5 % / Redundancy: 10.6 % / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 3.22→3.42 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4412 / CC1/2: 0.898

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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: 3.22→48.1 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1998 7.06 %
Rwork0.1856 26304 -
obs0.187 28302 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.22 Å2 / Biso mean: 76.821 Å2 / Biso min: 32.33 Å2
Refinement stepCycle: final / Resolution: 3.22→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 98 0 4522
Biso mean--75.83 --
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 (%)
3.22-3.30.36371320.30011745187794
3.3-3.390.28261390.260418461985100
3.39-3.490.28511410.240618581999100
3.49-3.60.281410.224618421983100
3.6-3.730.23751400.215718481988100
3.73-3.880.21991420.209418702012100
3.88-4.060.20711410.190318632004100
4.06-4.270.20691440.168318762020100
4.27-4.540.18621410.16118702011100
4.54-4.890.16971440.158918772021100
4.89-5.380.1831440.171419012045100
5.38-6.160.20191450.187819142059100
6.16-7.750.18181480.171619522100100
7.76-48.10.16381560.15612042219899

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