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- PDB-5k2o: Crystal structure of Arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 5k2o
TitleCrystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a pyrimidinyl-benzoate herbicide, pyrithiobac
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / pyrithiobac / thiamin diphosphate / FAD / pyrimidinyl-benzoate
Function / homology
Function and homology information


acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / 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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6QK / CITRIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Chem-TP9 / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.873 Å
AuthorsGarcia, M.D. / Lonhienne, T. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1008736 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families.
Authors: Garcia, M.D. / Nouwens, A. / Lonhienne, T.G. / Guddat, L.W.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)66,3336
Polymers64,5921
Non-polymers1,7415
Water7,098394
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)265,33124
Polymers258,3674
Non-polymers6,96420
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 area30670 Å2
ΔGint-217 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.090, 179.090, 184.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

21A-820-

HOH

31A-854-

HOH

41A-866-

HOH

51A-875-

HOH

61A-927-

HOH

71A-1051-

HOH

81A-1052-

HOH

91A-1058-

HOH

101A-1152-

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 / Plasmid: PET30A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 6 types, 399 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-6QK / 2-chloranyl-6-(4,6-dimethoxypyrimidin-2-yl)sulfanyl-benzoic acid


Mass: 326.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11ClN2O4S
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-TP9 / (3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE


Mass: 412.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N4O7P2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.6 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Sodium citrate, PEG 3350, FAD, ThDP, Magnesium chloride, DTT, Pyrithiobac

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2014 / Details: Mirrors
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 40366 / % possible obs: 99.9 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 41
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YHY

1yhy


Resolution: 2.873→40.299 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 1948 4.97 %Random selection
Rwork0.1465 ---
obs0.1481 39202 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.873→40.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 113 394 4987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024719
X-RAY DIFFRACTIONf_angle_d0.86423
X-RAY DIFFRACTIONf_dihedral_angle_d14.1721741
X-RAY DIFFRACTIONf_chiral_restr0.025706
X-RAY DIFFRACTIONf_plane_restr0.003836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.873-2.94480.38661340.30982571X-RAY DIFFRACTION95
2.9448-3.02440.29551340.27162581X-RAY DIFFRACTION97
3.0244-3.11340.27341410.25652631X-RAY DIFFRACTION97
3.1134-3.21380.26441330.23582590X-RAY DIFFRACTION96
3.2138-3.32860.25211360.21092650X-RAY DIFFRACTION98
3.3286-3.46180.25231380.19552613X-RAY DIFFRACTION97
3.4618-3.61930.23721320.17062596X-RAY DIFFRACTION96
3.6193-3.810.18371380.15052613X-RAY DIFFRACTION96
3.81-4.04850.15051350.12732608X-RAY DIFFRACTION96
4.0485-4.36070.13961430.10882637X-RAY DIFFRACTION97
4.3607-4.79890.13761400.09812682X-RAY DIFFRACTION98
4.7989-5.49180.11681430.10092724X-RAY DIFFRACTION98
5.4918-6.91350.14171460.12142807X-RAY DIFFRACTION99
6.9135-40.30260.14541550.11652951X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 63.5303 Å / Origin y: -62.5116 Å / Origin z: -12.7482 Å
111213212223313233
T0.3597 Å2-0.0571 Å2-0.0067 Å2-0.5174 Å2-0.0924 Å2--0.4586 Å2
L0.8719 °20.1225 °20.0701 °2-0.5998 °2-0.1859 °2--1.3091 °2
S-0.0762 Å °-0.2965 Å °0.0339 Å °0.1165 Å °-0.0719 Å °-0.0086 Å °-0.0848 Å °-0.0032 Å °0.1368 Å °
Refinement TLS groupSelection details: all

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