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- PDB-1t9d: Crystal Structure Of Yeast Acetohydroxyacid Synthase In Complex W... -

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Basic information

Entry
Database: PDB / ID: 1t9d
TitleCrystal Structure Of Yeast Acetohydroxyacid Synthase In Complex With A Sulfonylurea Herbicide, Metsulfuron methyl
ComponentsAcetolactate synthase, mitochondrial
KeywordsTRANSFERASE / acetohydroxyacid synthase / acetolactate synthase / herbicide / sulfonylurea / thiamin diphosphate / FAD / inhibitor / metsulfuron methyl
Function / homology
Function and homology information


acetolactate synthase / acetolactate synthase complex / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / amino acid biosynthetic process / 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-1MM / FLAVIN-ADENINE DINUCLEOTIDE / : / ETHYL DIHYDROGEN DIPHOSPHATE / PENTYL TRIHYDROGEN DIPHOSPHATE / 2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcCourt, J.A. / Pang, S.S. / Guddat, L.W. / Duggleby, R.G.
CitationJournal: Biochemistry / Year: 2005
Title: Elucidating the specificity of binding of sulfonylurea herbicides to acetohydroxyacid synthase.
Authors: McCourt, J.A. / Pang, S.S. / Guddat, L.W. / Duggleby, R.G.
History
DepositionMay 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_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_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
C: Acetolactate synthase, mitochondrial
D: Acetolactate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,71328
Polymers294,3914
Non-polymers6,32224
Water39,2012176
1
A: Acetolactate synthase, mitochondrial
B: Acetolactate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,39814
Polymers147,1952
Non-polymers3,20312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-53 kcal/mol
Surface area38180 Å2
MethodPISA
2
C: Acetolactate synthase, mitochondrial
D: Acetolactate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,31414
Polymers147,1952
Non-polymers3,11912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-65 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.347, 218.347, 361.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe assymetric unit contains 4 molecules arranged as two dimers. A dimer is the minimum biological unit required for activity.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetolactate synthase, mitochondrial / Acetohydroxy-acid synthase / ALS / AHAS


Mass: 73597.656 Da / Num. of mol.: 4 / Fragment: Catalytic Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILV2, SMR1, YMR108W, YM9718.07 / Plasmid: pET30(c) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07342, acetolactate synthase

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Non-polymers , 8 types, 2200 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-1MM / METHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE / METSULFURON METHYL


Mass: 381.364 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15N5O6S
#5: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical
ChemComp-PYD / 2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE


Mass: 123.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9N3
#7: Chemical ChemComp-P25 / PENTYL TRIHYDROGEN DIPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2
#8: Chemical ChemComp-P22 / ETHYL DIHYDROGEN DIPHOSPHATE


Mass: 206.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8O7P2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2176 / 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: 3.56 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium phosphate, thiamin diphosphate, FAD, magnesium chloride, DTT, metsulfuron methyl, Tris-HCl, Lithium sulfate, sodium potassium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2002 / Details: mirrors
RadiationMonochromator: GE (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.29→99 Å / Num. obs: 160659 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.5
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 5.71 / Num. unique all: 12195 / % possible all: 64

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Processing

Software
NameClassification
Adxvdata processing
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N0H

1n0h


Resolution: 2.3→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 15236 -RANDOM
Rwork0.164 ---
all0.167 160659 --
obs0.167 153191 80.1 %-
Displacement parametersBiso mean: 56.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.261 Å0.218 Å
Luzzati d res low-5 Å
Luzzati sigma a0.263 Å0.215 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17791 0 410 2176 20377
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.256 1109 -
Rwork0.215 --
obs-11557 64 %

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