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- PDB-5hs1: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -

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Basic information

Entry
Database: PDB / ID: 5hs1
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) complexed with Voriconazole
ComponentsLanosterol 14-alpha demethylase
Keywordsoxidoreductase/oxidoreductase inhibitor / Voriconazole / CYP51 / oxidoreductase-oxidoreducatse inhibitor complex / resistance mutation / oxidoreductase-oxidoreductase inhibitor complex
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 / molecular replacement / Resolution: 2.1 Å
AuthorsSabherwal, M. / Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Tyndall, J.D.A. / Monk, B.C.
Citation
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.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / 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, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)61,5543
Polymers60,5881
Non-polymers9662
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.010, 67.320, 81.090
Angle α, β, γ (deg.)90.000, 98.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 60587.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: ERG11, 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
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.1 / Details: 45% PEG 400, 0.1M GLYCINE / PH range: 9.1-9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→51.81 Å / Num. obs: 48392 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.14data scaling
PHASER2.6.0phasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.1→51.553 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 4794 5.07 %
Rwork0.204 89778 -
obs0.2058 48392 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.9 Å2 / Biso mean: 42.0333 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 2.1→51.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 68 167 4506
Biso mean--27.6 39.68 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084466
X-RAY DIFFRACTIONf_angle_d0.8786067
X-RAY DIFFRACTIONf_chiral_restr0.05641
X-RAY DIFFRACTIONf_plane_restr0.006786
X-RAY DIFFRACTIONf_dihedral_angle_d13.5552643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.31821580.31042946310498
2.1239-2.14890.29221810.29752933311498
2.1489-2.17510.36511590.28992954311398
2.1751-2.20260.32741670.27922946311398
2.2026-2.23160.31581640.28972977314198
2.2316-2.26220.33621620.31692885304797
2.2622-2.29450.31591450.28073048319399
2.2945-2.32870.35791850.25372946313199
2.3287-2.36510.29231410.24472993313499
2.3651-2.40390.27571270.23943039316699
2.4039-2.44540.27631560.22092976313299
2.4454-2.48980.26231640.214629653129100
2.4898-2.53770.22661600.215430183178100
2.5377-2.58950.19941480.216730563204100
2.5895-2.64580.25771300.206730023132100
2.6458-2.70740.29441810.221530413222100
2.7074-2.77510.26471550.216230053160100
2.7751-2.85010.24371350.209229573092100
2.8501-2.93390.25041670.205530553222100
2.9339-3.02860.26691820.200329983180100
3.0286-3.13690.23591690.20530043173100
3.1369-3.26240.22611550.214329933148100
3.2624-3.41090.24291690.195930073176100
3.4109-3.59070.22781500.190229913141100
3.5907-3.81560.21551740.182830313205100
3.8156-4.11010.24011740.179830153189100
4.1101-4.52350.18531680.164429893157100
4.5235-5.17750.21111450.166430543199100
5.1775-6.5210.22921790.188829783157100
6.521-51.56820.16071440.18232976312099

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