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- PDB-5v5z: Structure of CYP51 from the pathogen Candida albicans -

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Basic information

Entry
Database: PDB / ID: 5v5z
TitleStructure of CYP51 from the pathogen Candida albicans
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCATSE INHIBITOR / pathogen / Candida albicans / CYP51 / itraconazole / OXIDOREDUCTASE-OXIDOREDUCATSE INHIBITOR complex
Function / homology
Function and homology information


cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14-demethylase activity / sterol 14alpha-demethylase / ergosterol biosynthetic process / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / cellular response to xenobiotic stimulus / oxidoreductase activity ...cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14-demethylase activity / sterol 14alpha-demethylase / ergosterol biosynthetic process / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / cellular response to xenobiotic stimulus / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane / plasma 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 / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKeniya, M.V. / Sabherwal, M. / Wilson, R.K. / Sagatova, A.A. / 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: Crystal Structures of Full-Length Lanosterol 14 alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery.
Authors: Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Woods, M.A. / Sagatova, A.A. / Tyndall, J.D.A. / Monk, B.C.
#1: 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.
#2: 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
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 12, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.5Oct 4, 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)63,1713
Polymers61,8481
Non-polymers1,3222
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 92.510, 101.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Lanosterol 14-alpha demethylase / CYPLI / Cytochrome P450 51 / Cytochrome P450-14DM / Cytochrome P450-LIA1 / Sterol 14-alpha demethylase


Mass: 61848.430 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: ERG11, CYP51, ERG16, CAALFM_C500660CA, CaO19.922 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ADDELTA / References: UniProt: P10613, 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 / References: sterol 14alpha-demethylase / Comment: medication, antifungal*YM

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.5 M GLYCINE-NAOH, 35% PEG400,

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Data collection

DiffractionMean temperature: 91 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→91.94 Å / Num. obs: 19796 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3130 / CC1/2: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.9→44.505 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 968 4.91 %
Rwork0.219 --
obs0.2214 19726 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 92 0 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114221
X-RAY DIFFRACTIONf_angle_d1.2285740
X-RAY DIFFRACTIONf_dihedral_angle_d16.2562499
X-RAY DIFFRACTIONf_chiral_restr0.061597
X-RAY DIFFRACTIONf_plane_restr0.007760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.0530.39651410.35172618X-RAY DIFFRACTION100
3.053-3.24430.33191430.29822613X-RAY DIFFRACTION100
3.2443-3.49470.32741420.23362648X-RAY DIFFRACTION100
3.4947-3.84620.31281130.20422684X-RAY DIFFRACTION100
3.8462-4.40230.23331450.18922669X-RAY DIFFRACTION100
4.4023-5.54480.22061390.18642686X-RAY DIFFRACTION100
5.5448-44.50980.23931450.20982840X-RAY DIFFRACTION100

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