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- PDB-3ea4: Arabidopsis thaliana acetohydroxyacid synthase in complex with mo... -

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Basic information

Entry
Database: PDB / ID: 3ea4
TitleArabidopsis thaliana acetohydroxyacid synthase in complex with monosulfuron-ester
ComponentsAcetolactate synthase, chloroplastic
KeywordsTRANSFERASE / FAD and ThDP dependent enzyme / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Chloroplast / FAD / Flavoprotein / Herbicide resistance / Magnesium / Metal-binding / Thiamine pyrophosphate / Transit peptide
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-2SM / FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE / Chem-TDM / Acetolactate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsGuddat, L.W. / Wang, J.-G. / Li, Z.-M.
CitationJournal: Febs J. / Year: 2009
Title: Crystal structures of two novel sulfonylurea herbicides in complex with Arabidopsis thaliana acetohydroxyacid synthase.
Authors: Wang, J.-G. / Lee, P.K. / Dong, Y.-H. / Pang, S.S. / Duggleby, R.G. / Li, Z.-M. / Guddat, L.W.
History
DepositionAug 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Non-polymer description
Revision 1.3Nov 1, 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_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.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

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7456
Polymers63,8391
Non-polymers1,9065
Water1,946108
1
A: Acetolactate synthase, chloroplastic
hetero molecules

A: Acetolactate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,49012
Polymers127,6782
Non-polymers3,81210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area12670 Å2
ΔGint-117 kcal/mol
Surface area38900 Å2
MethodPISA
2
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)262,97924
Polymers255,3564
Non-polymers7,62420
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
Unit cell
Length a, b, c (Å)178.468, 178.468, 184.948
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-726-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetolactate synthase, chloroplastic /


Mass: 63838.926 Da / Num. of mol.: 1 / Fragment: residues 87-670
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSR 1.2, At3g48560, T8P19.70 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P17597, acetolactate synthase

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Non-polymers , 6 types, 113 molecules

#2: Chemical ChemComp-2SM / methyl 2-{[(4-methylpyrimidin-2-yl)carbamoyl]sulfamoyl}benzoate


Mass: 350.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N4O5S
#3: Chemical ChemComp-FAB / FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE


Mass: 855.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N9O16P2
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 0.1M CHES, 0.2M Li2SO4, 1M potassium sodium tartrate, 1mM ThDP, 1mM FAD, 1mM MgCl2, 5mM DTT, 1mM MSE , pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2005 / 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→58.42 Å / Num. all: 42923 / Num. obs: 42923 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 20.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 0 / Num. unique all: 4060 / Rsym value: 0.315 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YBH

1ybh


Resolution: 2.8→58.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.848 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.264 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21348 2153 5 %RANDOM
Rwork0.19895 ---
all0.19969 40611 --
obs0.19969 40611 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.026 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 120 108 4684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224704
X-RAY DIFFRACTIONr_angle_refined_deg1.1532.0016406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91824.495198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6581527
X-RAY DIFFRACTIONr_chiral_restr0.0770.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023568
X-RAY DIFFRACTIONr_nbd_refined0.1910.22161
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2204
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.212
X-RAY DIFFRACTIONr_mcbond_it0.3631.52988
X-RAY DIFFRACTIONr_mcangle_it0.65324697
X-RAY DIFFRACTIONr_scbond_it0.84631960
X-RAY DIFFRACTIONr_scangle_it1.4924.51708
LS refinement shellResolution: 2.797→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 136 -
Rwork0.311 2880 -
obs-136 95.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7312-0.4702-0.23421.2627-0.16721.7169-0.0928-0.02080.1840.1544-0.0116-0.2891-0.06910.27610.1044-0.14420.0035-0.0747-0.06760.0206-0.008572.397381.74734.3002
21.0614-0.3673-0.25641.3523-0.77652.45-0.1912-0.1110.13180.3760.1519-0.0026-0.2909-0.05440.0392-0.06990.0859-0.0305-0.1215-0.0291-0.103860.356178.444950.2328
31.3119-0.5102-0.1172.01110.05280.9749-0.2405-0.2892-0.06470.4940.17730.05580.1340.14350.06320.03630.1377-0.027-0.06390.0453-0.140566.942262.667256.0218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA87 - 1961 - 110
2X-RAY DIFFRACTION2AA197 - 369111 - 283
3X-RAY DIFFRACTION3AA370 - 582284 - 496

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