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- PDB-7ry9: S. CEREVISIAE CYP51 I471T mutant COMPLEXED WITH Voriconazole -

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Basic information

Entry
Database: PDB / ID: 7ry9
TitleS. CEREVISIAE CYP51 I471T mutant COMPLEXED WITH Voriconazole
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYP51 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / Sterol Biosynthesis / OXIDOREDUCTASE
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
PROTOPORPHYRIN IX CONTAINING FE / Voriconazole / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 14alpha-demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D. / Monk, B.C.
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

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0334
Polymers61,8731
Non-polymers1,1603
Water1,20767
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)76.790, 66.310, 80.730
Angle α, β, γ (deg.)90.000, 98.140, 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-VOR / Voriconazole / (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 349.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F3N5O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.2 / Details: 44% PEG 400, 0.5 M Glycine, pH 9.2 / 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: 2.4→33.15 Å / Num. obs: 31547 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 38.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 3119 / CC1/2: 0.719 / % possible all: 99.9

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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: 2.4→33.15 Å / SU ML: 0.2977 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 25.6162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 2859 4.67 %
Rwork0.2001 58416 -
obs0.2019 31538 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 81 67 4410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784469
X-RAY DIFFRACTIONf_angle_d0.92136066
X-RAY DIFFRACTIONf_chiral_restr0.0503639
X-RAY DIFFRACTIONf_plane_restr0.0082765
X-RAY DIFFRACTIONf_dihedral_angle_d16.58951662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.2781320.2842920X-RAY DIFFRACTION99.84
2.44-2.490.33311320.2752929X-RAY DIFFRACTION99.67
2.49-2.530.37481200.26472953X-RAY DIFFRACTION99.51
2.53-2.590.30391500.24872936X-RAY DIFFRACTION99.77
2.59-2.640.30651240.25652939X-RAY DIFFRACTION99.58
2.64-2.70.3271420.24672917X-RAY DIFFRACTION99.45
2.7-2.770.28311350.22932937X-RAY DIFFRACTION99.71
2.77-2.850.22561540.20662916X-RAY DIFFRACTION99.32
2.85-2.930.22631510.20452911X-RAY DIFFRACTION99.84
2.93-3.020.21981580.20062919X-RAY DIFFRACTION99.32
3.02-3.130.21311500.20592912X-RAY DIFFRACTION99.71
3.13-3.260.26011450.20472919X-RAY DIFFRACTION99.42
3.26-3.40.27751530.19692918X-RAY DIFFRACTION99.51
3.4-3.580.2481510.18612911X-RAY DIFFRACTION99.61
3.58-3.810.19881540.18172913X-RAY DIFFRACTION99.38
3.81-4.10.21851430.18612915X-RAY DIFFRACTION99.41
4.1-4.510.22351360.16692948X-RAY DIFFRACTION99.48
4.51-5.160.21321580.17372885X-RAY DIFFRACTION99.41
5.16-6.50.24081380.20742935X-RAY DIFFRACTION99.19
6.5-33.160.19871330.19092883X-RAY DIFFRACTION97.92

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