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- PDB-5k6q: Crystal structure of Arabidopsis thaliana acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 5k6q
TitleCrystal structure of Arabidopsis thaliana acetohydroxyacid synthase catalytic subunit
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / catalytic subunit / thiamin diphosphate / FAD
Function / homology
Function and homology information


acetolactate synthase activity / acetolactate synthase / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-TDM / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.952 Å
AuthorsGarcia, M.D. / Wang, J.-G. / Lonhienne, T. / Guddat, L.W.
CitationJournal: FEBS J. / Year: 2017
Title: Crystal structure of plant acetohydroxyacid synthase, the target for several commercial herbicides.
Authors: Garcia, M.D. / Wang, J.G. / Lonhienne, T. / Guddat, L.W.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)66,0775
Polymers64,5921
Non-polymers1,4864
Water3,207178
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)264,30920
Polymers258,3674
Non-polymers5,94216
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)132,15410
Polymers129,1832
Non-polymers2,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area12060 Å2
ΔGint-121 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.934, 178.934, 186.086
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-820-

HOH

21A-828-

HOH

31A-868-

HOH

41A-870-

HOH

51A-875-

HOH

61A-921-

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 , 5 types, 182 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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-TDM / 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE / 2-HYDROXYETHYLTHIAMIN DIPHOSPHATE


Mass: 468.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N4O8P2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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, lithium sulfate, CHES, FAD, ThDP, MgCl2

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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: Sep 25, 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: 2.95→44.56 Å / Num. obs: 37387 / % possible obs: 99.7 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 31.3
Reflection shellResolution: 2.95→3 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2.1 / % 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: 2.952→44.557 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.4
RfactorNum. reflection% reflection
Rfree0.2291 1838 5.29 %
Rwork0.1906 --
obs0.1926 34726 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.952→44.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 96 178 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024661
X-RAY DIFFRACTIONf_angle_d0.6036348
X-RAY DIFFRACTIONf_dihedral_angle_d12.2991718
X-RAY DIFFRACTIONf_chiral_restr0.024703
X-RAY DIFFRACTIONf_plane_restr0.003826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9521-3.03190.36781480.332553X-RAY DIFFRACTION95
3.0319-3.12110.3281480.30482530X-RAY DIFFRACTION95
3.1211-3.22180.33641400.30172509X-RAY DIFFRACTION93
3.2218-3.33690.32081420.28072522X-RAY DIFFRACTION95
3.3369-3.47050.34271410.25962513X-RAY DIFFRACTION94
3.4705-3.62840.27321380.2512495X-RAY DIFFRACTION92
3.6284-3.81960.2691270.22622407X-RAY DIFFRACTION89
3.8196-4.05870.2691270.20522380X-RAY DIFFRACTION88
4.0587-4.37190.22111350.16872372X-RAY DIFFRACTION87
4.3719-4.81140.17591370.14982481X-RAY DIFFRACTION91
4.8114-5.50650.19311390.15432568X-RAY DIFFRACTION93
5.5065-6.93340.20651530.16352677X-RAY DIFFRACTION96
6.9334-44.5620.15071630.13072881X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 63.3557 Å / Origin y: -62.1177 Å / Origin z: -13.1511 Å
111213212223313233
T0.3779 Å2-0.1055 Å2-0.038 Å2-0.6271 Å2-0.0515 Å2--0.4691 Å2
L2.421 °20.1197 °20.0661 °2-0.9658 °2-0.3332 °2--2.0533 °2
S-0.0319 Å °-0.6264 Å °-0.0624 Å °0.1732 Å °-0.0353 Å °-0.0294 Å °-0.0856 Å °0.0869 Å °0.0549 Å °
Refinement TLS groupSelection details: all

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