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- PDB-7ryx: S. CEREVISIAE CYP51 COMPLEXED WITH VT-1129 -

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Basic information

Entry
Database: PDB / ID: 7ryx
TitleS. CEREVISIAE CYP51 COMPLEXED WITH VT-1129
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / VT-1129 / 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-81H / 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
AuthorsRuma, Y.N. / Sagatova, A. / 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 / Year: 2022
Title: Characterisation of Candida parapsilosis CYP51 as a Drug Target Using Saccharomyces cerevisiae as Host.
Authors: Ruma, Y.N. / Keniya, M.V. / Tyndall, J.D.A. / Monk, B.C.
#1: 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.
#2: Journal: Antimicrob.Agents Chemother. / Year: 2019
Title: Azole Resistance Reduces Susceptibility to the Tetrazole Antifungal VT-1161.
Authors: Monk, B.C. / Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Graham, D.O. / Hassan, H.F. / Chen, D. / Tyndall, J.D.A.
History
DepositionAug 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)62,6013
Polymers61,4711
Non-polymers1,1302
Water73941
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)78.402, 67.978, 80.304
Angle α, β, γ (deg.)90.000, 99.381, 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: 61470.766 Da / Num. of mol.: 1
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-81H / (2R)-2-(2,4-difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-{5-[4-(trifluoromethoxy)phenyl]pyridin-2-yl}propan-2-ol


Mass: 513.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H14F7N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 44% PEG 400, 0.1 M Glycine, pH 9.5 / PH range: 9.3 - 9.5

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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 EIGER2 X 9M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→45.19 Å / Num. obs: 48767 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4018 / CC1/2: 0.893 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXv1.19.2-4158refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.1→45.19 Å / SU ML: 0.2663 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 35.5906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 4568 4.82 %
Rwork0.2336 90166 -
obs0.2353 48681 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 79 41 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794478
X-RAY DIFFRACTIONf_angle_d0.94126087
X-RAY DIFFRACTIONf_chiral_restr0.0529640
X-RAY DIFFRACTIONf_plane_restr0.0079794
X-RAY DIFFRACTIONf_dihedral_angle_d18.08461668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.37061310.32723107X-RAY DIFFRACTION99.2
2.12-2.150.40491300.30732948X-RAY DIFFRACTION99.64
2.15-2.180.34591240.30863123X-RAY DIFFRACTION99.66
2.18-2.20.33131190.28712996X-RAY DIFFRACTION99.39
2.2-2.230.33621610.29943028X-RAY DIFFRACTION99.41
2.23-2.260.31911260.28512976X-RAY DIFFRACTION99.2
2.26-2.290.33081850.28593013X-RAY DIFFRACTION99.07
2.29-2.330.32381260.28033007X-RAY DIFFRACTION99.21
2.33-2.370.31791730.28923023X-RAY DIFFRACTION99.35
2.37-2.40.30851620.28773009X-RAY DIFFRACTION99.19
2.4-2.450.34141610.28173011X-RAY DIFFRACTION99.34
2.45-2.490.32561860.28142906X-RAY DIFFRACTION98.88
2.49-2.540.34731780.27162972X-RAY DIFFRACTION98.96
2.54-2.590.30841580.2543037X-RAY DIFFRACTION99.53
2.59-2.650.37811430.2462969X-RAY DIFFRACTION99.46
2.65-2.710.26121630.24393022X-RAY DIFFRACTION99.31
2.71-2.780.2831370.25883039X-RAY DIFFRACTION99.41
2.78-2.850.29151670.25533012X-RAY DIFFRACTION99.53
2.85-2.930.3031430.25613015X-RAY DIFFRACTION99.4
2.93-3.030.33021450.27183004X-RAY DIFFRACTION99.65
3.03-3.140.31251470.26773018X-RAY DIFFRACTION99.15
3.14-3.260.33641630.26942998X-RAY DIFFRACTION99.03
3.26-3.410.28161200.2543029X-RAY DIFFRACTION98.56
3.41-3.590.29131390.24463003X-RAY DIFFRACTION98.9
3.59-3.820.27891580.23522973X-RAY DIFFRACTION98.43
3.82-4.110.22691490.21042994X-RAY DIFFRACTION99.09
4.11-4.520.21291870.19482966X-RAY DIFFRACTION98.78
4.52-5.180.26131760.18872969X-RAY DIFFRACTION99.02
5.18-6.520.2751570.21292995X-RAY DIFFRACTION98.78
6.52-45.190.17541540.19093004X-RAY DIFFRACTION99.21

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