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- PDB-9c4q: Crystal structure of wild-type arabidopsis thaliana acetohydroxya... -

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Basic information

Entry
Database: PDB / ID: 9c4q
TitleCrystal structure of wild-type arabidopsis thaliana acetohydroxyacid synthase in complex with newly designed herbicide FMO
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
: / ACETATE ION / Chem-AUJ / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / OXYGEN MOLECULE / L(+)-TARTARIC ACID / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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)67,04415
Polymers64,5921
Non-polymers2,45314
Water3,153175
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)268,17860
Polymers258,3674
Non-polymers9,81156
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 area33750 Å2
ΔGint-210 kcal/mol
Surface area69920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.664, 179.664, 185.437
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-706-

OXY

21A-712-

MG

31A-713-

MG

41A-832-

HOH

51A-918-

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 , 11 types, 189 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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 / Comment: pH buffer*YM
#5: 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
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-A1AUH / 2-(2-fluoroethoxy)-N-[(4-methoxy-6-methylpyrimidin-2-yl)carbamoyl]benzene-1-sulfonamide


Mass: 384.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17FN4O5S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.52→48.4 Å / Num. obs: 59670 / % possible obs: 99.6 % / Redundancy: 19.7 % / Biso Wilson estimate: 61.54 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 13.1
Reflection shellResolution: 2.52→2.59 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4359 / CC1/2: 0.852 / Rpim(I) all: 0.352

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→48.4 Å / SU ML: 0.3505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 1993 3.35 %
Rwork0.1727 57509 -
obs0.1736 59502 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.74 Å2
Refinement stepCycle: LAST / Resolution: 2.52→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 158 175 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234707
X-RAY DIFFRACTIONf_angle_d0.80676403
X-RAY DIFFRACTIONf_chiral_restr0.0437704
X-RAY DIFFRACTIONf_plane_restr0.0038832
X-RAY DIFFRACTIONf_dihedral_angle_d13.22871722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.38611300.33383793X-RAY DIFFRACTION93.36
2.58-2.650.30891410.27724044X-RAY DIFFRACTION99.71
2.65-2.730.27931390.24684056X-RAY DIFFRACTION99.83
2.73-2.820.29721410.22834061X-RAY DIFFRACTION99.9
2.82-2.920.23641420.22024077X-RAY DIFFRACTION99.98
2.92-3.040.2321410.21474092X-RAY DIFFRACTION99.93
3.04-3.180.21021420.18984072X-RAY DIFFRACTION99.79
3.18-3.340.22351410.18144080X-RAY DIFFRACTION99.93
3.34-3.550.20861420.1714110X-RAY DIFFRACTION99.98
3.55-3.830.17351440.16124127X-RAY DIFFRACTION99.98
3.83-4.210.15591440.14354156X-RAY DIFFRACTION100
4.21-4.820.14821440.12964159X-RAY DIFFRACTION99.98
4.82-6.070.20751480.16364229X-RAY DIFFRACTION100
6.07-48.40.18351540.16674453X-RAY DIFFRACTION99.96

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