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

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Basic information

Entry
Database: PDB / ID: 6dem
TitleCrystal structure of Candida albicans acetohydroxyacid synthase in complex with the herbicide bensulfuron methyl
ComponentsAcetolactate synthase
Keywordstransferase/transferase inhibitor / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiamin diphosphate / FAD / transferase / bensulfuron methyl / 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-60G / FLAVIN-ADENINE DINUCLEOTIDE / : / Chem-TP9 / Acetolactate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.038 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)75,9876
Polymers74,3151
Non-polymers1,6725
Water11,692649
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)303,94824
Polymers297,2614
Non-polymers6,68720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Unit cell
Length a, b, c (Å)175.414, 175.414, 177.527
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-812-

HOH

21A-1235-

HOH

31A-1269-

HOH

41A-1276-

HOH

51A-1284-

HOH

61A-1303-

HOH

71A-1332-

HOH

81A-1337-

HOH

91A-1342-

HOH

101A-1408-

HOH

111A-1420-

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 , 6 types, 654 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical ChemComp-60G / methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate / Bensulfuron methyl


Mass: 410.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O7S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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 bensulfuron methyl
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: 2.038→48.21 Å / Num. obs: 102110 / % possible obs: 99.7 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.04 / Rrim(I) all: 0.135 / Net I/σ(I): 15.6
Reflection shellResolution: 2.04→2.07 Å / Redundancy: 19 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4701 / Rpim(I) all: 0.293 / Rrim(I) all: 0.96 / % possible all: 94.3

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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: 2.038→43.984 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 1999 1.96 %
Rwork0.1461 --
obs0.1466 101924 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.038→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 108 649 5286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134823
X-RAY DIFFRACTIONf_angle_d1.3866581
X-RAY DIFFRACTIONf_dihedral_angle_d15.2841777
X-RAY DIFFRACTIONf_chiral_restr0.063740
X-RAY DIFFRACTIONf_plane_restr0.007848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0384-2.08940.26231360.22976792X-RAY DIFFRACTION96
2.0894-2.14590.21491400.20767055X-RAY DIFFRACTION100
2.1459-2.2090.22441420.20497056X-RAY DIFFRACTION100
2.209-2.28030.2511410.20717070X-RAY DIFFRACTION100
2.2803-2.36180.22641410.19197070X-RAY DIFFRACTION100
2.3618-2.45630.24081420.18427069X-RAY DIFFRACTION100
2.4563-2.56810.20051420.17527106X-RAY DIFFRACTION100
2.5681-2.70350.18071430.16497110X-RAY DIFFRACTION100
2.7035-2.87290.17641430.1627142X-RAY DIFFRACTION100
2.8729-3.09460.17031420.1547142X-RAY DIFFRACTION100
3.0946-3.40590.15551430.13797176X-RAY DIFFRACTION100
3.4059-3.89850.16051460.12027241X-RAY DIFFRACTION100
3.8985-4.91070.12681450.10187285X-RAY DIFFRACTION100
4.9107-43.9940.14521530.12257611X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 67.6262 Å / Origin y: 71.5698 Å / Origin z: 76.2391 Å
111213212223313233
T0.1387 Å20.0214 Å2-0.0466 Å2-0.2703 Å2-0.0465 Å2--0.2161 Å2
L0.7287 °2-0.2494 °20.1274 °2-0.766 °2-0.0478 °2--0.7619 °2
S-0.0116 Å °-0.2123 Å °0.066 Å °0.1011 Å °0.0055 Å °-0.0728 Å °-0.0745 Å °-0.0421 Å °-0.0915 Å °
Refinement TLS groupSelection details: all

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