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- PDB-5k6r: Crystal structure of Arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 5k6r
TitleCrystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a sulfonylamino-carbonyl-triazolinone herbicide, thiencarbazone-methyl
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiencarbazone methyl / thiamin diphosphate / FAD / sulfonylamino-carbonyl-triazolinone
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 (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-6R5 / FLAVIN-ADENINE DINUCLEOTIDE / : / Chem-TZD / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.734 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 25, 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.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

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4797
Polymers64,5921
Non-polymers1,8876
Water7,008389
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)265,91428
Polymers258,3674
Non-polymers7,54824
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
2
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,95714
Polymers129,1832
Non-polymers3,77412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area12350 Å2
ΔGint-97 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.364, 180.364, 186.467
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-705-

K

21A-811-

HOH

31A-836-

HOH

41A-911-

HOH

51A-918-

HOH

61A-947-

HOH

71A-1081-

HOH

81A-1151-

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, ILVB / 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, 395 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-6R5 / methyl 4-[(3-methoxy-4-methyl-5-oxidanylidene-1,2,4-triazol-1-yl)carbonylsulfamoyl]-5-methyl-thiophene-3-carboxylate


Mass: 390.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O7S2
#5: 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
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 9.8
Details: Na/K tartrate, CHES, ammonium sulfate, FAD, Thiamin diphosphate, MgCl2, DTT, Thiencarbazone-ethyl

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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 27, 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: 2.73→48.63 Å / Num. obs: 47622 / % possible obs: 99.6 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 10.2
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YHY

1yhy


Resolution: 2.734→44.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.08
RfactorNum. reflection% reflection
Rfree0.1781 1998 4.2 %
Rwork0.1446 --
obs0.146 47539 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.734→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 120 389 4961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024692
X-RAY DIFFRACTIONf_angle_d0.6836392
X-RAY DIFFRACTIONf_dihedral_angle_d13.8041729
X-RAY DIFFRACTIONf_chiral_restr0.026703
X-RAY DIFFRACTIONf_plane_restr0.003830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7339-2.80230.26671320.24213019X-RAY DIFFRACTION95
2.8023-2.8780.26921400.22353217X-RAY DIFFRACTION100
2.878-2.96270.26951420.20893214X-RAY DIFFRACTION100
2.9627-3.05830.19831410.18993216X-RAY DIFFRACTION100
3.0583-3.16760.19661410.18713213X-RAY DIFFRACTION100
3.1676-3.29430.21691410.18493217X-RAY DIFFRACTION100
3.2943-3.44420.20921410.17743225X-RAY DIFFRACTION100
3.4442-3.62570.18341430.15433252X-RAY DIFFRACTION100
3.6257-3.85280.18681420.13633238X-RAY DIFFRACTION100
3.8528-4.15010.15091430.12273266X-RAY DIFFRACTION100
4.1501-4.56730.14841450.11333279X-RAY DIFFRACTION100
4.5673-5.22740.15441450.10683305X-RAY DIFFRACTION100
5.2274-6.58250.16911470.12593357X-RAY DIFFRACTION100
6.5825-44.67580.14311550.12813523X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 63.7106 Å / Origin y: -62.8677 Å / Origin z: -13.1144 Å
111213212223313233
T0.2844 Å2-0.0594 Å2-0.0405 Å2-0.3817 Å2-0.0385 Å2--0.3285 Å2
L1.4824 °20.1384 °20.1858 °2-0.8909 °2-0.2832 °2--1.5347 °2
S0.0033 Å °-0.3694 Å °0.045 Å °0.2091 Å °-0.0545 Å °-0.0366 Å °-0.1023 Å °0.0991 Å °0.0452 Å °
Refinement TLS groupSelection details: all

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