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- PDB-5k3s: Crystal structure of Arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 5k3s
TitleCrystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a pyrimidinyl-benzoate herbicide, bispyribac-sodium
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / bispyribac-sodium / thiamin diphosphate / FAD / pyrimidinyl-benzoate
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
Chem-6QL / 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 ...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.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.value / _struct_conn.pdbx_dist_value / _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

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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)66,2445
Polymers64,5921
Non-polymers1,6534
Water6,107339
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)264,97720
Polymers258,3674
Non-polymers6,61016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Unit cell
Length a, b, c (Å)179.715, 179.715, 184.775
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-801-

HOH

21A-824-

HOH

31A-832-

HOH

41A-872-

HOH

51A-930-

HOH

61A-948-

HOH

71A-991-

HOH

81A-1024-

HOH

91A-1028-

HOH

101A-1050-

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 , 5 types, 343 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-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-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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 6.6 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Potassium citrate, PEG 3350, FAD, ThDP, Magnesium chloride, DTT, Bispyribac

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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: Jul 17, 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: 2.87→42.04 Å / Num. obs: 40616 / % possible obs: 99.9 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 37.5
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 3.9 / % 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→42.034 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1869 4.89 %Random selection
Rwork0.1731 ---
obs0.1749 38248 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.873→42.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 110 339 4914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024732
X-RAY DIFFRACTIONf_angle_d0.7126447
X-RAY DIFFRACTIONf_dihedral_angle_d13.6081754
X-RAY DIFFRACTIONf_chiral_restr0.023709
X-RAY DIFFRACTIONf_plane_restr0.003840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8731-2.95080.5181370.35872657X-RAY DIFFRACTION91
2.9508-3.03760.33861350.30252675X-RAY DIFFRACTION92
3.0376-3.13560.31631350.28482687X-RAY DIFFRACTION92
3.1356-3.24770.30911370.26362710X-RAY DIFFRACTION93
3.2477-3.37760.26541470.22082774X-RAY DIFFRACTION95
3.3776-3.53130.2491490.21142802X-RAY DIFFRACTION95
3.5313-3.71740.20781410.1782765X-RAY DIFFRACTION94
3.7174-3.95010.18711360.16752740X-RAY DIFFRACTION93
3.9501-4.25480.20731420.15352724X-RAY DIFFRACTION92
4.2548-4.68250.16441500.12822832X-RAY DIFFRACTION95
4.6825-5.35890.14361420.1272885X-RAY DIFFRACTION96
5.3589-6.74710.18291560.14622959X-RAY DIFFRACTION97
6.7471-42.03880.15711620.12713169X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 86.1549 Å / Origin y: -23.7123 Å / Origin z: -18.031 Å
111213212223313233
T0.4874 Å20.0152 Å2-0.0115 Å2-0.3263 Å2-0.047 Å2--0.3792 Å2
L0.6138 °2-0.1273 °2-0.2988 °2-1.1582 °20.0171 °2--1.2099 °2
S0.0127 Å °0.2006 Å °-0.0904 Å °-0.3053 Å °-0.0678 Å °0.0307 Å °0.1677 Å °-0.0698 Å °0.0493 Å °
Refinement TLS groupSelection details: all

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