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- PDB-5ead: Saccharomyces cerevisiae CYP51 complexed with the plant pathogen ... -

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Basic information

Entry
Database: PDB / ID: 5ead
TitleSaccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor S-desthio-prothioconazole
ComponentsLanosterol 14-alpha demethylase
KeywordsOxidoreductase/Oxidoreducatse inhibitor / CYP51 / S-desthio-prothioconazole / oxidoreductase-oxidoreductase inhibitor complex / Oxidoreductase-Oxidoreducatse 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
Chem-5L9 / PROTOPORPHYRIN IX CONTAINING FE / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTyndall, J.D.A. / Sabherwal, M. / Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Woods, M.V. / Monk, B.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Bayer CropScience Germany
Citation
Journal: PLoS ONE / Year: 2016
Title: Structural and Functional Elucidation of Yeast Lanosterol 14 alpha-Demethylase in Complex with Agrochemical Antifungals.
Authors: Tyndall, J.D. / Sabherwal, M. / Sagatova, A.A. / Keniya, M.V. / Negroni, J. / Wilson, R.K. / Woods, M.A. / Tietjen, K. / Monk, B.C.
#1: 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
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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)62,8143
Polymers61,8851
Non-polymers9292
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.270, 67.180, 80.910
Angle α, β, γ (deg.)90.000, 99.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61885.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SDE is the small molecule S-desthio-prothioconazole
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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-5L9 / (2~{S})-2-(1-chloranylcyclopropyl)-1-(2-chlorophenyl)-3-(1,2,4-triazol-1-yl)propan-2-ol / S-desthio-prothioconazole


Mass: 312.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15Cl2N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 45% PEG 400, 0.1M GLYCINE / PH range: 9.4-9.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→30.267 Å / Num. obs: 56012 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.04 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8 / Num. measured all: 219677 / Scaling rejects: 167
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.053.90.731.41620641310.810.4299.4
8.94-79.893.70.0413.223306310.9970.02393

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å30.27 Å
Translation7.76 Å30.27 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.7data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2→30.267 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2820 5.04 %
Rwork0.1945 103902 -
obs0.196 55946 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.53 Å2 / Biso mean: 43.7354 Å2 / Biso min: 20.89 Å2
Refinement stepCycle: final / Resolution: 2→30.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 63 152 4492
Biso mean--28.84 41.05 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094476
X-RAY DIFFRACTIONf_angle_d1.1016083
X-RAY DIFFRACTIONf_chiral_restr0.045643
X-RAY DIFFRACTIONf_plane_restr0.005780
X-RAY DIFFRACTIONf_dihedral_angle_d14.3831662
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 (%)
2-2.02280.33371890.31523582377199
2.0228-2.04660.37031760.31063362353899
2.0466-2.07150.34551650.29933492365799
2.0715-2.09770.32551790.28353455363499
2.0977-2.12530.25252010.275934403641100
2.1253-2.15440.32491930.26623515370899
2.1544-2.18520.28581920.25013425361799
2.1852-2.21780.27811960.246234193615100
2.2178-2.25240.2981890.25143449363899
2.2524-2.28940.24911750.24783495367099
2.2894-2.32880.30632070.21534083615100
2.3288-2.37120.211630.20963493365699
2.3712-2.41670.23671540.206734823636100
2.4167-2.46610.22461890.195835003689100
2.4661-2.51960.21311960.199434643660100
2.5196-2.57820.21841590.204334873646100
2.5782-2.64270.28371600.197734393599100
2.6427-2.71410.28082050.20134833688100
2.7141-2.79390.21491500.19643520367099
2.7939-2.8840.2051730.186134653638100
2.884-2.9870.21942140.175733983612100
2.987-3.10650.17772060.191334963702100
3.1065-3.24770.24711700.201234703640100
3.2477-3.41870.25661920.196834663658100
3.4187-3.63260.19891710.187234773648100
3.6326-3.91250.20242070.170634573664100
3.9125-4.30520.19862080.164534523660100
4.3052-4.92590.16591630.14873463362699
4.9259-6.19740.20052070.18433418362599
6.1974-30.270.20671650.17773430359598

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