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- PDB-7rya: S. CEREVISIAE CYP51 I471T MUTANT COMPLEXED WITH ITRACONAZOLE -

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Basic information

Entry
Database: PDB / ID: 7rya
TitleS. CEREVISIAE CYP51 I471T MUTANT COMPLEXED WITH ITRACONAZOLE
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYP51 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / Sterol Biosynthesis / OXIDOREDUCTASE
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: 2.1 Å
AuthorsGraham, D.O. / Wilson, R.K. / Ruma, Y.N. / Keniya, M.V. / Tyndall, J.D. / Monk, B.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC)16/232 New Zealand
Health Research Council (HRC)19/397 New Zealand
Citation
Journal: J Fungi (Basel) / Year: 2021
Title: Structural Insights into the Azole Resistance of the Candida albicans Darlington Strain Using Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase as a Surrogate.
Authors: Graham, D.O. / Wilson, R.K. / Ruma, Y.N. / Keniya, M.V. / Tyndall, J.D.A. / Monk, B.C.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / 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 3rd, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1953
Polymers61,8731
Non-polymers1,3222
Water3,531196
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)77.530, 66.700, 80.580
Angle α, β, γ (deg.)90.000, 98.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61873.160 Da / Num. of mol.: 1 / Mutation: I471T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Variant: 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 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 44% PEG 400, 0.5 M Glycine, pH 9.5 / PH range: 9.1 - 9.6

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Data collection

DiffractionMean temperature: 91 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→33.42 Å / Num. obs: 45698 / % possible obs: 95.73 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 4038 / CC1/2: 0.836 / % possible all: 85.33

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.1→33.42 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.9483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 4659 5.28 %
Rwork0.1982 83631 -
obs0.2002 45680 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 92 196 4568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774504
X-RAY DIFFRACTIONf_angle_d0.89666121
X-RAY DIFFRACTIONf_chiral_restr0.0536645
X-RAY DIFFRACTIONf_plane_restr0.0069806
X-RAY DIFFRACTIONf_dihedral_angle_d16.69781689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.31971390.26552443X-RAY DIFFRACTION83
2.12-2.150.30891480.26932453X-RAY DIFFRACTION83.63
2.15-2.180.31411470.25492459X-RAY DIFFRACTION84.2
2.18-2.20.26441520.26542477X-RAY DIFFRACTION85.33
2.2-2.230.42791690.34252518X-RAY DIFFRACTION85.63
2.23-2.260.421330.39142538X-RAY DIFFRACTION86.95
2.26-2.290.42421550.32672604X-RAY DIFFRACTION87.78
2.29-2.330.3231410.23552658X-RAY DIFFRACTION89.51
2.33-2.370.25181220.23052693X-RAY DIFFRACTION91.13
2.37-2.40.26791560.22642668X-RAY DIFFRACTION91.6
2.4-2.450.26241520.2092800X-RAY DIFFRACTION93.71
2.45-2.490.28391420.212798X-RAY DIFFRACTION94.35
2.49-2.540.22411680.21932739X-RAY DIFFRACTION95.78
2.54-2.590.24021370.2092927X-RAY DIFFRACTION97.21
2.59-2.650.25661870.21512837X-RAY DIFFRACTION97.55
2.65-2.710.25021500.22452889X-RAY DIFFRACTION98.48
2.71-2.770.24261650.21432938X-RAY DIFFRACTION99.01
2.77-2.850.24941530.20262935X-RAY DIFFRACTION99.2
2.85-2.930.24791790.19012883X-RAY DIFFRACTION99.74
2.93-3.030.2621650.19892940X-RAY DIFFRACTION99.9
3.03-3.140.23571940.19232898X-RAY DIFFRACTION99.9
3.14-3.260.24021720.20342942X-RAY DIFFRACTION100
3.26-3.410.24191690.19412958X-RAY DIFFRACTION99.97
3.41-3.590.20451480.17512939X-RAY DIFFRACTION99.97
3.59-3.810.20781310.16562982X-RAY DIFFRACTION99.87
3.81-4.110.23041580.16672959X-RAY DIFFRACTION99.87
4.11-4.520.17431410.14992960X-RAY DIFFRACTION100
4.52-5.170.17521990.15782911X-RAY DIFFRACTION99.94
5.17-6.50.20681080.18512989X-RAY DIFFRACTION99.81
6.51-33.420.19631790.18172896X-RAY DIFFRACTION98.94

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