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- PDB-1n0h: Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex w... -

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Basic information

Entry
Database: PDB / ID: 1n0h
TitleCrystal Structure of Yeast Acetohydroxyacid Synthase in Complex with a Sulfonylurea Herbicide, Chlorimuron Ethyl
ComponentsAcetolactate synthase
KeywordsLYASE / ACETOHYDROXYACID SYNTHASE / SULFONYLUREA / HERBICIDE INHIBITION / THIAMINE DIPHOSPHATE
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / 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-AYD / Chem-CIE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / FLAVIN-ADENINE DINUCLEOTIDE / : / THIAMINE DIPHOSPHATE / Acetolactate synthase catalytic subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPang, S.S. / Guddat, L.W. / Duggleby, R.G.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Molecular basis of sulfonylurea herbicide inhibition of acetohydroxyacid synthase
Authors: Pang, S.S. / Guddat, L.W. / Duggleby, R.G.
History
DepositionOct 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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_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
B: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,83914
Polymers147,1952
Non-polymers3,64412
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint-99 kcal/mol
Surface area38750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.976, 153.976, 178.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsThe biological unit is a dimer, which is the same assembly found in the asymmetric unit of the crystal structure

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 73597.656 Da / Num. of mol.: 2 / Fragment: MATURE CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILV2 / Plasmid: pET30c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07342, EC: 4.1.3.18

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Non-polymers , 8 types, 844 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CIE / 2-[[[[(4-CHLORO-6-METHOXY-2-PYRIMIDINYL)AMINO]CARBONYL]AMINO]SULFONYL]BENZOIC ACID ETHYL ESTER / CHLORIMURON ETHYL


Mass: 414.821 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15ClN4O6S
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-AYD / 4-{[(4'-AMINO-2'-METHYLPYRIMIDIN-5'-YL)METHYL]AMINO}PENT-3-ENYL DIPHOSPHATE


Mass: 382.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N4O7P2
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: POTASSIUM PHOSPHATE, THIAMINE DIPHOSPHATE, FAD, MAGNESIUM CHLORIDE, DTT, CHLORIMURON ETHYL, TRIS-HCL, LITHIUM SULFATE, SODIUM POTASSIUM TARTRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mMThDP1reservoir
21 mM1reservoirMgCl2
31 mMFAD1reservoir
41 mMCE1reservoir
55 mMdithiothreitol1reservoir
60.2 Mpotassium phosphate1reservoirpH7.0
70.1 MTris-HCl1reservoirpH7.0
80.2 M1reservoirLi2SO4
90.9 Msodium potassium tartrate1reservoir

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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: Jul 25, 2002 / 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: 2.8→48.7 Å / Num. obs: 52457 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4769 / % possible all: 81.5
Reflection
*PLUS
Num. measured all: 571130
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 81.5 % / Num. unique obs: 4769 / Num. measured obs: 15211

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Processing

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

1jsc


Resolution: 2.8→48.7 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5203 -RANDOM
Rwork0.163 ---
all0.168 50877 --
obs0.168 50877 95.3 %-
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.179 Å2-3.179 Å26.358 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9134 0 230 832 10196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.278 386 -
Rwork0.246 --
obs-3856 73.7 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å

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