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

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Basic information

Entry
Database: PDB / ID: 5esh
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) G73W mutant in complex with itraconazole
ComponentsLanosterol 14-alpha demethylase
Keywordsoxidoreductase/oxidoreductase inhibitor / CYP51 / mutation / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase activity / methylation / iron ion binding / heme binding / endoplasmic reticulum / membrane
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-1YN / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
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)63,3363
Polymers62,0141
Non-polymers1,3222
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.560, 66.850, 80.880
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 62014.371 Da / Num. of mol.: 1 / Mutation: G73W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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-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 / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 63.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG-400 45%, 0.1 M glycine / PH range: 9.3-9.5

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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: 2.15→80.02 Å / Num. obs: 44569 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.3
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

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

4lxj


Resolution: 2.15→29.949 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2247 5.05 %
Rwork0.1827 --
obs0.1847 44525 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 92 149 4522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094508
X-RAY DIFFRACTIONf_angle_d1.1246125
X-RAY DIFFRACTIONf_dihedral_angle_d13.9331689
X-RAY DIFFRACTIONf_chiral_restr0.045645
X-RAY DIFFRACTIONf_plane_restr0.006805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.19670.27871480.24962610X-RAY DIFFRACTION99
2.1967-2.24780.27241440.23682613X-RAY DIFFRACTION100
2.2478-2.3040.26631480.23012646X-RAY DIFFRACTION100
2.304-2.36630.27941210.20622626X-RAY DIFFRACTION100
2.3663-2.43590.27271300.19882647X-RAY DIFFRACTION100
2.4359-2.51450.24331480.19272609X-RAY DIFFRACTION100
2.5145-2.60430.22681240.18362662X-RAY DIFFRACTION100
2.6043-2.70850.22921410.18312638X-RAY DIFFRACTION100
2.7085-2.83170.27061320.18122634X-RAY DIFFRACTION100
2.8317-2.98080.221460.18522663X-RAY DIFFRACTION100
2.9808-3.16740.21941440.19112625X-RAY DIFFRACTION100
3.1674-3.41170.24851450.18592664X-RAY DIFFRACTION100
3.4117-3.75440.19921410.1722645X-RAY DIFFRACTION99
3.7544-4.29630.2181550.16552648X-RAY DIFFRACTION100
4.2963-5.40770.19671410.16072652X-RAY DIFFRACTION99
5.4077-29.95190.18951390.18552696X-RAY DIFFRACTION98

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