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

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Basic information

Entry
Database: PDB / ID: 5esm
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) T322I mutant complexed with fluconazole
ComponentsLanosterol 14-alpha demethylase
Keywordsoxidoreductase/oxidoreductase inhibitor / CYP51 / 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 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: To Be Published
Title: Structures of lanosterol 14-alpha demethylase mutants.
Authors: Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / 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 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

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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)62,8203
Polymers61,8971
Non-polymers9232
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-19 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.370, 67.640, 81.040
Angle α, β, γ (deg.)90.00, 99.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61897.270 Da / Num. of mol.: 1 / Mutation: T322I
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.: 202 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / 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: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→51.67 Å / Num. obs: 57073 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2→29.91 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 2874 5.04 %
Rwork0.2027 --
obs0.2043 57073 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 65 202 4539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044466
X-RAY DIFFRACTIONf_angle_d0.8036063
X-RAY DIFFRACTIONf_dihedral_angle_d13.0221659
X-RAY DIFFRACTIONf_chiral_restr0.03640
X-RAY DIFFRACTIONf_plane_restr0.003784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.37541380.34642582X-RAY DIFFRACTION100
2.0328-2.06780.33631220.32852546X-RAY DIFFRACTION100
2.0678-2.10540.34471350.29362557X-RAY DIFFRACTION100
2.1054-2.14590.28261420.27512574X-RAY DIFFRACTION100
2.1459-2.18970.28111370.25962600X-RAY DIFFRACTION100
2.1897-2.23730.3131530.24072538X-RAY DIFFRACTION100
2.2373-2.28930.26131340.23652561X-RAY DIFFRACTION99
2.2893-2.34650.26851470.22492572X-RAY DIFFRACTION100
2.3465-2.410.27061110.21312596X-RAY DIFFRACTION100
2.41-2.48080.22951370.20322577X-RAY DIFFRACTION100
2.4808-2.56090.22061340.19672566X-RAY DIFFRACTION100
2.5609-2.65240.22511250.20282590X-RAY DIFFRACTION99
2.6524-2.75850.25261330.19832569X-RAY DIFFRACTION100
2.7585-2.88390.23411310.20442584X-RAY DIFFRACTION99
2.8839-3.03580.23161500.19962576X-RAY DIFFRACTION100
3.0358-3.22580.2061380.20312592X-RAY DIFFRACTION100
3.2258-3.47460.26181430.2022587X-RAY DIFFRACTION100
3.4746-3.82360.21071380.19042593X-RAY DIFFRACTION99
3.8236-4.37540.20391560.17542596X-RAY DIFFRACTION100
4.3754-5.50690.19211340.17252631X-RAY DIFFRACTION100
5.5069-29.91350.22851360.19282612X-RAY DIFFRACTION97

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