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- PDB-7tzz: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 7tzz
TitleCrystal structure of arabidopsis thaliana acetohydroxyacid synthase P197T mutant in complex with bispyribac-sodium
ComponentsAcetolactate synthase, chloroplastic
KeywordsLIGASE / Herbicide / Resistance / AHAS / ALS
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-6QL / Chem-AUJ / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGuddat, L.W. / Cheng, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of resistance to herbicides that target acetohydroxyacid synthase.
Authors: Lonhienne, T. / Cheng, Y. / Garcia, M.D. / Hu, S.H. / Low, Y.S. / Schenk, G. / Williams, C.M. / Guddat, L.W.
History
DepositionFeb 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,76212
Polymers63,5241
Non-polymers2,23711
Water5,116284
1
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,52324
Polymers127,0492
Non-polymers4,47422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area12000 Å2
ΔGint-145 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.558, 179.558, 184.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
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-

MG

21A-707-

MG

31A-711-

MG

41A-860-

HOH

51A-880-

HOH

61A-969-

HOH

71A-1045-

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: 63524.488 Da / Num. of mol.: 1 / Mutation: P197T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALS, AHAS, CSR1, TZP5, At3g48560, T8P19.70 / Production host: Escherichia coli (E. coli) / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 8 types, 295 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / 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-6QL / 2,6-bis[(4,6-dimethoxypyrimidin-2-yl)oxy]benzoic acid


Mass: 430.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N4O8
#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: isolated from a genetically manipulated source
Formula: C14H23N4O10P2S
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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

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: 0.954 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.59→48.29 Å / Num. obs: 55052 / % possible obs: 99.6 % / Redundancy: 20.1 % / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 22.9
Reflection shellResolution: 2.59→2.66 Å / Num. unique obs: 4274 / CC1/2: 0.943 / Rpim(I) all: 0.153 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2O

5k2o


Resolution: 2.59→44.89 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 1999 3.64 %
Rwork0.1546 52981 -
obs0.1549 54980 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.66 Å2 / Biso mean: 63.1424 Å2 / Biso min: 38.17 Å2
Refinement stepCycle: final / Resolution: 2.59→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 143 284 4875
Biso mean--59.95 66.73 -
Num. residues----582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.59-2.650.26531350.23633575371096
2.65-2.720.27591410.200737303871100
2.72-2.80.20631410.192437493890100
2.8-2.890.17041410.185237343875100
2.89-30.21141410.178837373878100
3-3.120.23441410.180737363877100
3.12-3.260.19471430.188737603903100
3.26-3.430.18531410.175137543895100
3.43-3.650.17631420.163137763918100
3.65-3.930.15451440.14738023946100
3.93-4.320.11321440.125538103954100
4.32-4.950.12921440.120838423986100
4.95-6.230.16221480.151438864034100
6.23-44.890.15441530.150540904243100

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