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- PDB-9c85: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 9c85
TitleCrystal structure of arabidopsis thaliana acetohydroxyacid synthase in complex with 2022-LS5
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / Inhibitor / complex / AHAS / ALS / herbicide
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 / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsGao, Y. / Guddat, L.W.
Funding support China, Australia, 5items
OrganizationGrant numberCountry
Other government2023YFD1700403 China
Other government22277060 China
Other government21977057 China
Other government Australia
Other government Australia
CitationJournal: To Be Published
Title: Crystal structure of arabidopsis thaliana acetohydroxyacid synthase in complex with 2022-LS5
Authors: Gao, Y. / Guddat, L.W.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7018
Polymers64,5921
Non-polymers2,1097
Water37821
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)266,80332
Polymers258,3674
Non-polymers8,43628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area30210 Å2
ΔGint-304 kcal/mol
Surface area70750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.740, 178.740, 185.490
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

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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
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P17597, acetolactate synthase

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Non-polymers , 7 types, 28 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1AU7 / 2-(3-fluoropropoxy)-N-[(4-methoxy-6-methylpyrimidin-2-yl)carbamoyl]benzene-1-sulfonamide


Mass: 398.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19FN4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#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-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
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 2-(N-cyclohexylamino)-ethanesulfonic acid (CHES), (NH4)2SO4 and potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.72→36.22 Å / Num. obs: 47414 / % possible obs: 99.9 % / Redundancy: 20.1 % / Biso Wilson estimate: 79.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.8
Reflection shellResolution: 2.72→2.78 Å / Num. unique obs: 2735 / CC1/2: 0.662 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2v1.0data reduction
Aimless0.7.7data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→36.08 Å / SU ML: 0.4109 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2024 2335 4.93 %
Rwork0.1791 45029 -
obs0.1802 47364 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.23 Å2
Refinement stepCycle: LAST / Resolution: 2.72→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 135 21 4616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01274695
X-RAY DIFFRACTIONf_angle_d1.32746390
X-RAY DIFFRACTIONf_chiral_restr0.2555699
X-RAY DIFFRACTIONf_plane_restr0.0247823
X-RAY DIFFRACTIONf_dihedral_angle_d17.06621716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.780.42891440.37152591X-RAY DIFFRACTION100
2.78-2.840.33081380.31622612X-RAY DIFFRACTION100
2.84-2.90.3481370.30662589X-RAY DIFFRACTION100
2.9-2.970.3141330.26512593X-RAY DIFFRACTION100
2.97-3.050.29351420.25162600X-RAY DIFFRACTION100
3.05-3.140.27341310.24192630X-RAY DIFFRACTION100
3.14-3.250.27181180.24242637X-RAY DIFFRACTION99.96
3.25-3.360.29051390.22752602X-RAY DIFFRACTION100
3.36-3.50.24681430.20712617X-RAY DIFFRACTION100
3.5-3.660.22251270.1842642X-RAY DIFFRACTION100
3.66-3.850.17781420.17262622X-RAY DIFFRACTION99.96
3.85-4.090.20651310.16232660X-RAY DIFFRACTION99.96
4.09-4.40.17461570.13942631X-RAY DIFFRACTION100
4.4-4.850.17711320.13672683X-RAY DIFFRACTION100
4.85-5.550.17651310.15912696X-RAY DIFFRACTION100
5.55-6.980.1891340.18222750X-RAY DIFFRACTION100
6.98-36.080.15171560.14882874X-RAY DIFFRACTION99.74

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