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- PDB-6del: Crystal structure of Candida albicans acetohydroxyacid synthase i... -

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Basic information

Entry
Database: PDB / ID: 6del
TitleCrystal structure of Candida albicans acetohydroxyacid synthase in complex with the herbicide chlorimuron ethyl
ComponentsAcetolactate synthase
Keywordstransferase/transferase inhibitor / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiamin diphosphate / FAD / transferase / chlorimuron ethyl / sulfonylurea / transferase-transferase inhibitor complex
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / 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-CIE / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / Chem-G8G / : / Chem-TP9 / Acetolactate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.119 Å
AuthorsGarcia, M.D. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1008736 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Commercial AHAS-inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections.
Authors: Garcia, M.D. / Chua, S.M.H. / Low, Y.S. / Lee, Y.T. / Agnew-Francis, K. / Wang, J.G. / Nouwens, A. / Lonhienne, T. / Williams, C.M. / Fraser, J.A. / Guddat, L.W.
History
DepositionMay 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4808
Polymers74,3151
Non-polymers2,1647
Water10,016556
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)305,91932
Polymers297,2614
Non-polymers8,65828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Unit cell
Length a, b, c (Å)176.306, 176.306, 177.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

21A-1202-

HOH

31A-1218-

HOH

41A-1241-

HOH

51A-1244-

HOH

61A-1270-

HOH

71A-1335-

HOH

81A-1336-

HOH

91A-1348-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetolactate synthase


Mass: 74315.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ILV2, orf19.1613, CAALFM_C302320WA / Plasmid: pET30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D8PJF9, acetolactate synthase

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Non-polymers , 8 types, 563 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C15H15ClN4O6S
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-TP9 / (3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE


Mass: 412.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N4O7P2S
#7: Chemical ChemComp-G8G / (3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl](formyl)amino}-3-sulfanylpent-3-en-1-yl trihydrogen diphosphate


Mass: 442.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O8P2S
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 5.37 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1 mM FAD, 1 mM ThDP, 5 mM MgCl2, 5 mM DTT, 3 mM sodium pyruvate, 1 M Na/K tartrate, 0.1 M CHES, and 0.2 M ammonium sulfate, 1 mM chlorimuron ethyl
PH range: 9.4-9.8

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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: Mar 19, 2016 / 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: 2.119→48.39 Å / Num. obs: 91976 / % possible obs: 99.7 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.051 / Rrim(I) all: 0.169 / Net I/σ(I): 11.3
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.895 / Num. unique obs: 4219 / Rpim(I) all: 0.291 / Rrim(I) all: 0.942 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DEK

6dek


Resolution: 2.119→46.794 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 1998 2.17 %
Rwork0.1627 --
obs0.1632 91864 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.119→46.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 137 556 5212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054820
X-RAY DIFFRACTIONf_angle_d1.0586576
X-RAY DIFFRACTIONf_dihedral_angle_d14.8151783
X-RAY DIFFRACTIONf_chiral_restr0.035741
X-RAY DIFFRACTIONf_plane_restr0.004843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1193-2.17230.27741350.25486062X-RAY DIFFRACTION96
2.1723-2.23110.29041410.24596354X-RAY DIFFRACTION100
2.2311-2.29670.25881420.23716344X-RAY DIFFRACTION100
2.2967-2.37080.29261410.2276330X-RAY DIFFRACTION100
2.3708-2.45560.28711400.21716392X-RAY DIFFRACTION100
2.4556-2.55390.29021430.21376361X-RAY DIFFRACTION100
2.5539-2.67010.24081420.19676390X-RAY DIFFRACTION100
2.6701-2.81090.20781410.19266373X-RAY DIFFRACTION100
2.8109-2.98690.22591430.18236436X-RAY DIFFRACTION100
2.9869-3.21750.18641430.16516424X-RAY DIFFRACTION100
3.2175-3.54120.15581440.14646455X-RAY DIFFRACTION100
3.5412-4.05340.14521450.12736498X-RAY DIFFRACTION100
4.0534-5.10580.12081450.1126583X-RAY DIFFRACTION100
5.1058-46.80560.15761530.14046864X-RAY DIFFRACTION100

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