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- PDB-5wj1: Crystal structure of Arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 5wj1
TitleCrystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a triazolopyrimidine herbicide, penoxsulam
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / ThDP / FAD / thiamine aminoethenethiol diphosphate / triazolopyrimidine / penoxsulam
Function / homology
Function and homology information


acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / amino acid biosynthetic process / chloroplast ...acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / amino acid biosynthetic process / chloroplast / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion
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
ETHANEPEROXOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / Chem-PXD / Chem-TP9 / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.522 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: 2018
Title: Structural insights into the mechanism of inhibition of AHAS by herbicides.
Authors: Lonhienne, T. / Garcia, M.D. / Pierens, G. / Mobli, M. / Nouwens, A. / Guddat, L.W.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)66,3807
Polymers64,5601
Non-polymers1,8216
Water11,962664
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)265,52128
Polymers258,2394
Non-polymers7,28324
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)179.957, 179.957, 185.350
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-703-

K

21A-811-

HOH

31A-934-

HOH

41A-1048-

HOH

51A-1202-

HOH

61A-1268-

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: 64559.664 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 , 7 types, 670 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PXD / 2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl)benzenesulfonamide / Penoxsulam


Mass: 483.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F5N5O5S
#6: Chemical ChemComp-F50 / ETHANEPEROXOIC ACID / Peracetic acid


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

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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: 6.7 Å3/Da / Density % sol: 81.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis Tris propane, PEG 3350, FAD, ThDP, Magnesium chloride, DTT, Penoxsulam

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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: Oct 9, 2015 / 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: 2.52→48.41 Å / Num. obs: 59731 / % possible obs: 99.9 % / Redundancy: 21.5 % / CC1/2: 0.9 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.042 / Net I/σ(I): 16.1
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4350 / CC1/2: 0.963 / Rpim(I) all: 0.222 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2O

5k2o


Resolution: 2.522→44.416 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.54
RfactorNum. reflection% reflection
Rfree0.1653 1992 3.35 %
Rwork0.1397 --
obs0.1406 59458 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.522→44.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 117 664 5235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034757
X-RAY DIFFRACTIONf_angle_d0.7466486
X-RAY DIFFRACTIONf_dihedral_angle_d14.7311765
X-RAY DIFFRACTIONf_chiral_restr0.027706
X-RAY DIFFRACTIONf_plane_restr0.003839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5224-2.58550.23951330.2223833X-RAY DIFFRACTION94
2.5855-2.65540.2091390.18944034X-RAY DIFFRACTION100
2.6554-2.73350.22881420.18684082X-RAY DIFFRACTION100
2.7335-2.82170.18981410.18094052X-RAY DIFFRACTION100
2.8217-2.92250.20341420.17764078X-RAY DIFFRACTION100
2.9225-3.03950.19231400.16424095X-RAY DIFFRACTION100
3.0395-3.17780.2031410.16194063X-RAY DIFFRACTION100
3.1778-3.34530.19751430.15484085X-RAY DIFFRACTION100
3.3453-3.55480.20291420.14194113X-RAY DIFFRACTION100
3.5548-3.82910.15321430.13184093X-RAY DIFFRACTION99
3.8291-4.21420.16041430.11754125X-RAY DIFFRACTION99
4.2142-4.82340.11391420.1014145X-RAY DIFFRACTION99
4.8234-6.07450.13891470.12374222X-RAY DIFFRACTION100
6.0745-44.42270.12921540.12544446X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 63.6504 Å / Origin y: -63.0895 Å / Origin z: -12.6425 Å
111213212223313233
T0.2233 Å2-0.0459 Å2-0.0361 Å2-0.3307 Å2-0.0253 Å2--0.2675 Å2
L0.8077 °20.0942 °20.1151 °2-0.4951 °2-0.1726 °2--0.9234 °2
S0.013 Å °-0.2884 Å °0.0692 Å °0.1096 Å °-0.047 Å °-0.039 Å °-0.1116 Å °0.1066 Å °0.0291 Å °
Refinement TLS groupSelection details: all

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