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- PDB-5esf: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -

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Basic information

Entry
Database: PDB / ID: 5esf
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) G73E mutant complexed with fluconazole
ComponentsLanosterol 14-alpha demethylase
Keywordsoxidoreductase/oxidoreductase inhibitor / CYP51 / oxidoreductase-oxidoreducatse inhibitor complex / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-TPF / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / 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: Antimicrob.Agents Chemother. / Year: 2018
Title: Impact of Homologous Resistance Mutations from Pathogenic Yeast on Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Tyndall, J.D.A. / 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.
#2: Journal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)62,8803
Polymers61,9571
Non-polymers9232
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.490, 66.930, 81.060
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61957.270 Da / Num. of mol.: 1 / Mutation: G73E
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, sterol 14alpha-demethylase
#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-TPF / 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL / FLUCONAZOLE / ALPHA-(2,4-DIFLUOROPHENYL)-ALPHA-(1H-1,2,4-TRIAZOLE-1-YLMETHYL)-1H-1,2,4-TRIAZOLE-1-ETHANOL / ELAZOR / TRIFLUCAN / BIOZOLENE


Mass: 306.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12F2N6O / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / 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 315r / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→79.97 Å / Num. obs: 39044 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.5
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.25→38.719 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1954 5 %
Rwork0.2092 --
obs0.2113 39044 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→38.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 65 107 4417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044437
X-RAY DIFFRACTIONf_angle_d0.8466022
X-RAY DIFFRACTIONf_dihedral_angle_d13.5961650
X-RAY DIFFRACTIONf_chiral_restr0.031636
X-RAY DIFFRACTIONf_plane_restr0.003779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.45661260.43672368X-RAY DIFFRACTION89
2.3063-2.36860.33421350.29062643X-RAY DIFFRACTION100
2.3686-2.43830.34011170.25912697X-RAY DIFFRACTION100
2.4383-2.5170.27771590.23782654X-RAY DIFFRACTION100
2.517-2.60690.23241270.22782661X-RAY DIFFRACTION100
2.6069-2.71130.33821430.262672X-RAY DIFFRACTION99
2.7113-2.83460.3041180.21692673X-RAY DIFFRACTION100
2.8346-2.9840.24551570.21042657X-RAY DIFFRACTION100
2.984-3.17090.24761470.21622681X-RAY DIFFRACTION100
3.1709-3.41560.2781440.21252679X-RAY DIFFRACTION100
3.4156-3.75910.2221370.20242664X-RAY DIFFRACTION99
3.7591-4.30240.24091620.18572646X-RAY DIFFRACTION99
4.3024-5.41820.21151390.17112674X-RAY DIFFRACTION99
5.4182-38.72490.22171430.18822721X-RAY DIFFRACTION98

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