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- PDB-9c4p: Crystal structure of wild-type arabidopsis thaliana acetohydroxya... -

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Basic information

Entry
Database: PDB / ID: 9c4p
TitleCrystal structure of wild-type arabidopsis thaliana acetohydroxyacid synthase in complex with commercial herbicide triasulfuron
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / Herbicide / Resistance / AHAS / ALS / LIGASE
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
: / Chem-AUJ / FLAVIN-ADENINE DINUCLEOTIDE / S,R MESO-TARTARIC ACID / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCheng, Y. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Crystal Structures of Arabidopsis thaliana Acetohydroxyacid Synthase in Complex with the Herbicide Triasulfuron and Two Analogues with Herbicidal Activity in Field Trials.
Authors: Cheng, Y. / Wang, Y. / Lonhienne, T. / Wang, J.G. / Guddat, L.W.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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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)66,97511
Polymers64,5921
Non-polymers2,38310
Water4,720262
1
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,89844
Polymers258,3674
Non-polymers9,53240
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area31750 Å2
ΔGint-290 kcal/mol
Surface area69470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.704, 178.704, 184.806
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-707-

MG

21A-816-

HOH

31A-851-

HOH

41A-964-

HOH

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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: 64591.664 Da / Num. of mol.: 1 / Fragment: UNP residues 86-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALS, AHAS, CSR1, TZP5, At3g48560, T8P19.70, ILVB / Production host: Escherichia coli (E. coli) / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 8 types, 272 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-A1AUE / 2-(2-chloroethoxy)-N-[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)carbamoyl]benzene-1-sulfonamide


Mass: 401.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16ClN5O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AUJ / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 501.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N4O10P2S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

CrystalDescription: Yellow diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.8
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: 0.95372 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.4→48.19 Å / Num. obs: 68463 / % possible obs: 99.9 % / Redundancy: 19.7 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.45 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4494 / CC1/2: 0.841 / Rpim(I) all: 0.28 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.19 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 1998 2.92 %
Rwork0.1715 66384 -
obs0.172 68382 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 150 262 4868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254721
X-RAY DIFFRACTIONf_angle_d0.80336428
X-RAY DIFFRACTIONf_chiral_restr0.0432706
X-RAY DIFFRACTIONf_plane_restr0.0043832
X-RAY DIFFRACTIONf_dihedral_angle_d12.52721734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.32981380.3044617X-RAY DIFFRACTION98.69
2.46-2.520.28111410.26394658X-RAY DIFFRACTION99.94
2.52-2.60.27191410.23184675X-RAY DIFFRACTION99.96
2.6-2.680.2221410.21684671X-RAY DIFFRACTION100
2.68-2.780.23531400.2124679X-RAY DIFFRACTION100
2.78-2.890.20931420.21144706X-RAY DIFFRACTION99.96
2.89-3.020.23031410.214695X-RAY DIFFRACTION99.96
3.02-3.180.23671420.19934708X-RAY DIFFRACTION100
3.18-3.380.20491410.18474724X-RAY DIFFRACTION99.98
3.38-3.640.19671430.17824743X-RAY DIFFRACTION100
3.64-4.010.18131430.15994756X-RAY DIFFRACTION100
4.01-4.580.16891450.1324807X-RAY DIFFRACTION100
4.58-5.770.15231460.14324851X-RAY DIFFRACTION99.96
5.77-48.190.1531540.1525094X-RAY DIFFRACTION99.92

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