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- PDB-6dek: Crystal structure of Candida albicans acetohydroxyacid synthase c... -

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Basic information

Entry
Database: PDB / ID: 6dek
TitleCrystal structure of Candida albicans acetohydroxyacid synthase catalytic subunit
ComponentsAcetolactate synthase
Keywordstransferase/transferase inhibitor / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiamin diphosphate / FAD / transferase / 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
FLAVIN-ADENINE DINUCLEOTIDE / : / THIAMINE DIPHOSPHATE / Acetolactate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.971 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

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Assembly

Deposited unit
A: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5905
Polymers74,3151
Non-polymers1,2744
Water1,54986
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)302,35920
Polymers297,2614
Non-polymers5,09716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_575x,x-y+2,-z+1/31
Buried area24620 Å2
ΔGint-191 kcal/mol
Surface area78980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.039, 176.039, 177.626
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-880-

HOH

21A-885-

HOH

31A-886-

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 , 5 types, 90 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-TPP / THIAMINE DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 86 / 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: 5.35 Å3/Da / Density % sol: 77.02 %
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 sodium sulfate
PH range: 9.4-9.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 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: 2.97→49.13 Å / Num. obs: 33165 / % possible obs: 97.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.069 / Rrim(I) all: 0.16 / Net I/σ(I): 9.6
Reflection shellResolution: 2.97→3.12 Å / Redundancy: 6 % / Rmerge(I) obs: 0.792 / Num. unique obs: 4342 / Rpim(I) all: 0.385 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T9B

1t9b


Resolution: 2.971→49.128 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06
RfactorNum. reflection% reflection
Rfree0.1858 1999 6.04 %
Rwork0.1533 --
obs0.1553 33110 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.971→49.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 81 86 4676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034740
X-RAY DIFFRACTIONf_angle_d0.7216465
X-RAY DIFFRACTIONf_dihedral_angle_d14.4681756
X-RAY DIFFRACTIONf_chiral_restr0.025737
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9714-3.04570.31851370.28322143X-RAY DIFFRACTION96
3.0457-3.1280.2721430.2352235X-RAY DIFFRACTION99
3.128-3.220.25461420.21772192X-RAY DIFFRACTION99
3.22-3.3240.26661430.20442229X-RAY DIFFRACTION99
3.324-3.44270.23941420.18882212X-RAY DIFFRACTION99
3.4427-3.58050.20141440.17072233X-RAY DIFFRACTION99
3.5805-3.74340.18291420.16272217X-RAY DIFFRACTION98
3.7434-3.94070.18561410.1412204X-RAY DIFFRACTION98
3.9407-4.18750.16421450.13492237X-RAY DIFFRACTION98
4.1875-4.51060.16681420.11842213X-RAY DIFFRACTION97
4.5106-4.96410.14981410.10972206X-RAY DIFFRACTION96
4.9641-5.68150.15931430.1312233X-RAY DIFFRACTION96
5.6815-7.15460.17651450.14912239X-RAY DIFFRACTION96
7.1546-49.13460.1471490.13712318X-RAY DIFFRACTION93

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