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- PDB-8et4: Crystal structure of wild-type arabidopsis thaliana acetohydroxya... -

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Basic information

Entry
Database: PDB / ID: 8et4
TitleCrystal structure of wild-type arabidopsis thaliana acetohydroxyacid synthase in complex with amidosulfuron
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 / L(+)-TARTARIC ACID / Chem-WRQ / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGuddat, L.W. / Cheng, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Crystal Structure of the Commercial Herbicide, Amidosulfuron, in Complex with Arabidopsis thaliana Acetohydroxyacid Synthase.
Authors: Cheng, Y. / Lonhienne, T. / Garcia, M.D. / Williams, C.M. / Schenk, G. / Guddat, L.W.
History
DepositionOct 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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)66,87011
Polymers64,5921
Non-polymers2,27910
Water181
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)267,48144
Polymers258,3674
Non-polymers9,11540
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
Unit cell
Length a, b, c (Å)179.026, 179.026, 185.032
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-708-

MG

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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, 11 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 / Comment: FAD*YM
#4: Chemical ChemComp-WRQ / N-{[(4,6-dimethoxypyrimidin-2-yl)carbamoyl]sulfamoyl}-N-methylmethanesulfonamide


Mass: 369.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O7S2
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#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-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
#8: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 6.74 Å3/Da / Density % sol: 81.74 % / Description: 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: 0.979 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: 2.95→48.26 Å / Num. obs: 37363 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 66.48 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 17.3
Reflection shellResolution: 2.95→3.08 Å / Redundancy: 13.3 % / Num. unique obs: 4409 / CC1/2: 0.918 / Rpim(I) all: 0.251 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2O

5k2o


Resolution: 2.95→48.26 Å / SU ML: 0.3071 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 1999 5.35 %
Rwork0.1801 35331 -
obs0.1814 37330 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.6 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 143 1 4604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234705
X-RAY DIFFRACTIONf_angle_d0.76736407
X-RAY DIFFRACTIONf_chiral_restr0.0423705
X-RAY DIFFRACTIONf_plane_restr0.004829
X-RAY DIFFRACTIONf_dihedral_angle_d11.98161731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.020.31591380.26732428X-RAY DIFFRACTION97.9
3.02-3.10.26491410.25682487X-RAY DIFFRACTION99.96
3.1-3.20.26551400.25642484X-RAY DIFFRACTION99.85
3.2-3.30.27111400.23982471X-RAY DIFFRACTION100
3.3-3.420.24961400.21582482X-RAY DIFFRACTION100
3.42-3.550.25671410.21072498X-RAY DIFFRACTION100
3.55-3.710.21851430.19922505X-RAY DIFFRACTION99.96
3.71-3.910.21641410.19262510X-RAY DIFFRACTION100
3.91-4.160.20261440.16962523X-RAY DIFFRACTION100
4.16-4.480.17891420.14422526X-RAY DIFFRACTION99.96
4.48-4.930.17981430.14372526X-RAY DIFFRACTION99.96
4.93-5.640.19391450.1592560X-RAY DIFFRACTION99.93
5.64-7.10.1911470.1732598X-RAY DIFFRACTION99.93
7.1-48.260.15451540.15342733X-RAY DIFFRACTION99.18

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