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- PDB-7ry8: S. CEREVISIAE CYP51 Y140H mutant COMPLEXED WITH Voriconazole -

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Basic information

Entry
Database: PDB / ID: 7ry8
TitleS. CEREVISIAE CYP51 Y140H 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


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
beta-D-glucopyranose / PROTOPORPHYRIN IX CONTAINING FE / Voriconazole / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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.
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)63,2445
Polymers61,8601
Non-polymers1,3844
Water2,216123
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)77.790, 66.863, 80.878
Angle α, β, γ (deg.)90.000, 98.509, 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

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61860.184 Da / Num. of mol.: 1 / Mutation: Y140H
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
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 126 molecules

#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
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6 / Details: 46% PEG, 0.5 M glycine pH 9.6 / 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: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.98→44.68 Å / Num. obs: 57294 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Net I/σ(I): 7.2
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 3.302 / Num. unique obs: 4026 / CC1/2: 0.317 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless1.19.2_4158data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 1.98→39.99 Å / SU ML: 0.2607 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1391 2.44 %
Rwork0.2093 55729 -
obs0.21 57120 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.53 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 96 123 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724480
X-RAY DIFFRACTIONf_angle_d0.84576080
X-RAY DIFFRACTIONf_chiral_restr0.0519645
X-RAY DIFFRACTIONf_plane_restr0.0072764
X-RAY DIFFRACTIONf_dihedral_angle_d15.31461668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.35721380.36215410X-RAY DIFFRACTION97.3
2.05-2.130.38091360.32115542X-RAY DIFFRACTION99.68
2.13-2.230.29841400.28715577X-RAY DIFFRACTION99.97
2.23-2.350.29461390.26055525X-RAY DIFFRACTION99.84
2.35-2.490.27341350.23015596X-RAY DIFFRACTION99.91
2.49-2.690.25561450.21355605X-RAY DIFFRACTION99.9
2.69-2.960.2541340.20095547X-RAY DIFFRACTION99.93
2.96-3.380.2391400.19755616X-RAY DIFFRACTION99.95
3.39-4.260.20341420.18715615X-RAY DIFFRACTION99.84
4.26-39.990.20841420.19245696X-RAY DIFFRACTION99.34

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