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- PDB-1yi1: Crystal structure of Arabidopsis thaliana Acetohydroxyacid syntha... -

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Basic information

Entry
Database: PDB / ID: 1yi1
TitleCrystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Tribenuron methyl
ComponentsAcetolactate synthase
KeywordsTRANSFERASE / Acetohydroxyacid synthase / acetolactate synthase / herbicide / sulfonylurea / thiamin diphosphate / FAD / inhibitor / cysteine-s-dioxide / CHES / tribenuron methyl
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
Chem-1TB / FLAVIN-ADENINE DINUCLEOTIDE / ETHYL DIHYDROGEN DIPHOSPHATE / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsMcCourt, J.A. / Pang, S.S. / King-Scott, J. / Guddat, L.W. / Duggleby, R.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase
Authors: McCourt, J.A. / Pang, S.S. / King-Scott, J. / Guddat, L.W. / Duggleby, R.G.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / struct_conn_type / struct_ref_seq_dif / struct_site
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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2106
Polymers64,5921
Non-polymers1,6195
Water3,675204
1
A: Acetolactate synthase
hetero molecules

A: Acetolactate synthase
hetero molecules

A: Acetolactate synthase
hetero molecules

A: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,84124
Polymers258,3674
Non-polymers6,47420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
MethodPQS
2
A: Acetolactate synthase
hetero molecules

A: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,42012
Polymers129,1832
Non-polymers3,23710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area12840 Å2
ΔGint-102 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.060, 179.060, 186.145
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological unit is a tetramer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetolactate synthase / / Acetohydroxy-acid synthase / ALS


Mass: 64591.664 Da / Num. of mol.: 1 / Fragment: residues 86-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ILVB / Plasmid: pET30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 6 types, 209 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-1TB / METHYL 2-[4-METHOXY-6-METHYL-1,3,5-TRAZIN-2-YL(METHYL)CARBAMOYLSULFAMOYL]BENZOATE / TRIBENURON METHYL


Mass: 395.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N5O6S
#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-P22 / ETHYL DIHYDROGEN DIPHOSPHATE


Mass: 206.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8O7P2
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 80.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Tris, FAD, DTT, ThDP, magnesium chloride, tribenuron methyl, CHES, lithium sufate, potassium sodium tartrate, pH 9.0-9.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2003 / Details: mirrors
RadiationMonochromator: GE(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 35505 / Num. obs: 35505 / % possible obs: 90.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3276 / % possible all: 85.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YBH

1ybh


Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3326 10 %random
Rwork0.1868 ---
all0.1906 35505 --
obs0.1906 33393 84.5 %-
Displacement parametersBiso mean: 57.058 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.398 Å0.3242 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.4506 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 105 204 4727
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.3952 256 -
Rwork0.3317 --
obs-2478 86.5 %

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