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- PDB-4zdy: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -

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Basic information

Entry
Database: PDB / ID: 4zdy
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140F mutant complexed with itraconazole
ComponentsLanosterol 14-alpha demethylase
Keywordsoxidoreductase/oxidoreductase inhibitor / Itraconazole / CYP51 / oxidoreductase-oxidoreducatse inhibitor complex / resistance mutation / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


sterol 14alpha-demethylase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / iron ion binding / heme binding / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1YN / PROTOPORPHYRIN IX CONTAINING FE / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSagatova, A. / Keniya, M.V. / Wilson, R.K. / Tyndall, J.D.A. / Monk, B.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Marsden Fund New Zealand
Citation
Journal: Sci Rep / Year: 2016
Title: Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14 alpha-demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D. / Monk, B.C.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Non-polymer description / Structure summary
Revision 1.3Aug 9, 2017Group: Data collection / Database references
Category: diffrn_source / pdbx_database_related / pdbx_related_exp_data_set
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_database_related.details
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1913
Polymers61,8691
Non-polymers1,3222
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.180, 67.070, 80.700
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61869.215 Da / Num. of mol.: 1 / Mutation: Y140F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2Delta / References: UniProt: A6ZSR0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1YN / 2-[(2R)-butan-2-yl]-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one / Itraconazole


Mass: 705.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38Cl2N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 45% PEG 400, 0.1 M Glycine / PH range: 9.3 - 9.55

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→34.27 Å / Num. obs: 54071 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.9
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.3 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Blu-Icedata collection
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.02→33.37 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2724 5.04 %
Rwork0.191 --
obs0.193 54031 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 92 187 4541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084496
X-RAY DIFFRACTIONf_angle_d1.046108
X-RAY DIFFRACTIONf_dihedral_angle_d14.0521687
X-RAY DIFFRACTIONf_chiral_restr0.046643
X-RAY DIFFRACTIONf_plane_restr0.005805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.05670.36311460.28462631X-RAY DIFFRACTION98
2.0567-2.09630.30241280.30282642X-RAY DIFFRACTION98
2.0963-2.13910.25521480.23292613X-RAY DIFFRACTION99
2.1391-2.18560.26221440.222712X-RAY DIFFRACTION99
2.1856-2.23640.26251590.222728X-RAY DIFFRACTION100
2.2364-2.29230.27751260.25862644X-RAY DIFFRACTION100
2.2923-2.35430.24491580.18752657X-RAY DIFFRACTION100
2.3543-2.42350.22491120.18532748X-RAY DIFFRACTION100
2.4235-2.50170.21931570.17512711X-RAY DIFFRACTION100
2.5017-2.59110.2151340.1822689X-RAY DIFFRACTION100
2.5911-2.69480.24791330.182745X-RAY DIFFRACTION100
2.6948-2.81740.24211300.1812693X-RAY DIFFRACTION100
2.8174-2.96590.22911540.18422705X-RAY DIFFRACTION100
2.9659-3.15150.20811500.19392699X-RAY DIFFRACTION100
3.1515-3.39470.2431530.19362722X-RAY DIFFRACTION100
3.3947-3.73590.20561380.18152737X-RAY DIFFRACTION100
3.7359-4.27550.21821640.16712690X-RAY DIFFRACTION100
4.2755-5.3830.18661420.16342755X-RAY DIFFRACTION100
5.383-33.37750.22931480.18822786X-RAY DIFFRACTION99

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