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- PDB-7ryb: S. CEREVISIAE CYP51 Y140H/I471T - double mutant COMPLEXED WITH Vo... -

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Basic information

Entry
Database: PDB / ID: 7ryb
TitleS. CEREVISIAE CYP51 Y140H/I471T - double 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
PROTOPORPHYRIN IX CONTAINING FE / Voriconazole / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8143
Polymers61,8481
Non-polymers9662
Water181
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)79.180, 67.300, 81.330
Angle α, β, γ (deg.)90.000, 99.790, 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: 61848.129 Da / Num. of mol.: 1 / Mutation: Y140H, 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6 / Details: 46% PEG 400, 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: 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: 2.9→33.75 Å / Num. obs: 18602 / % possible obs: 98.21 % / Redundancy: 7.4 % / Biso Wilson estimate: 54.02 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.566 / Num. unique obs: 1830 / CC1/2: 0.753

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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: 2.9→33.75 Å / SU ML: 0.4273 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.2693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 1713 4.8 %
Rwork0.2028 33943 -
obs0.2052 18592 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4228 0 68 1 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094422
X-RAY DIFFRACTIONf_angle_d1.05216008
X-RAY DIFFRACTIONf_chiral_restr0.0518635
X-RAY DIFFRACTIONf_plane_restr0.0079759
X-RAY DIFFRACTIONf_dihedral_angle_d20.33351642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.39911410.31192822X-RAY DIFFRACTION97.15
2.99-3.080.41641150.29282864X-RAY DIFFRACTION96.82
3.08-3.190.35611560.28872796X-RAY DIFFRACTION96.88
3.19-3.320.3171460.25922822X-RAY DIFFRACTION97.06
3.32-3.470.25691150.22322833X-RAY DIFFRACTION97.36
3.47-3.650.27491440.20192832X-RAY DIFFRACTION97.06
3.65-3.880.25051140.19762865X-RAY DIFFRACTION97.51
3.88-4.180.25081360.18312836X-RAY DIFFRACTION97.38
4.18-4.60.20221860.1642795X-RAY DIFFRACTION97.77
4.6-5.260.20482080.172780X-RAY DIFFRACTION97.77
5.27-6.630.24191010.19722891X-RAY DIFFRACTION97.87
6.63-34.430.22591510.17342807X-RAY DIFFRACTION96.6

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