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

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Basic information

Entry
Database: PDB / ID: 5esn
TitleSaccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) T322I mutant structure
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / CYP51
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 / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D.A. / Monk, B.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Marsden Fund New Zealand
Citation
Journal: To Be Published
Title: Structures of lanosterol 14-alpha demethylase mutants.
Authors: Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D.A. / 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.
#2: Journal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,5142
Polymers61,8971
Non-polymers6161
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-27 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.520, 65.950, 80.950
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61897.270 Da / Num. of mol.: 1 / Mutation: T322I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2Delta / References: UniProt: A6ZSR0, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 45% PEG-400, 0.1 M Glycine / PH range: 9.3-9.55

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→79.99 Å / Num. obs: 33722 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Blu-Icedata collection
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.35→38.3 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 1700 5.04 %
Rwork0.1835 --
obs0.1857 33722 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 43 100 4415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084441
X-RAY DIFFRACTIONf_angle_d0.8986029
X-RAY DIFFRACTIONf_dihedral_angle_d14.0412622
X-RAY DIFFRACTIONf_chiral_restr0.049639
X-RAY DIFFRACTIONf_plane_restr0.006763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41920.28191260.21052651X-RAY DIFFRACTION100
2.4192-2.49720.24591560.19612629X-RAY DIFFRACTION100
2.4972-2.58650.23111230.1872676X-RAY DIFFRACTION100
2.5865-2.690.25911390.18732663X-RAY DIFFRACTION100
2.69-2.81240.24041320.18692670X-RAY DIFFRACTION100
2.8124-2.96060.25011520.18182634X-RAY DIFFRACTION100
2.9606-3.1460.22761410.19052693X-RAY DIFFRACTION100
3.146-3.38880.22771490.19552668X-RAY DIFFRACTION100
3.3888-3.72960.23011430.17832661X-RAY DIFFRACTION99
3.7296-4.26860.21621560.16942666X-RAY DIFFRACTION100
4.2686-5.37570.21861400.16552678X-RAY DIFFRACTION99
5.3757-38.30470.21381430.19932733X-RAY DIFFRACTION98

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