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

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Basic information

Entry
Database: PDB / ID: 5eac
TitleSaccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor R-tebuconazole
ComponentsLanosterol 14-alpha demethylase
KeywordsOxidoreductase/Oxidoreducatse inhibitor / CYP51 / R-tebuconazole / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-TBQ / sterol 14alpha-demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 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

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8103
Polymers61,8851
Non-polymers9242
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-26 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.370, 67.330, 80.790
Angle α, β, γ (deg.)90.000, 98.560, 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
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-TBQ / (3~{R})-1-(4-chlorophenyl)-4,4-dimethyl-3-(1,2,4-triazol-1-ylmethyl)pentan-3-ol / (R)-tebuconazole


Mass: 307.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22ClN3O / Details: TBQ is the small molecule R-tebuconazole
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 45% PEG 400, 0.1M GLYCINE

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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: 2.26→29.944 Å / Num. obs: 38587 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 40.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.052 / Net I/σ(I): 9.7 / Num. measured all: 150826 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.26-2.330.991.51344335510.6310.57999.3
9.04-79.890.02531.624176340.9990.01597.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.74 Å51.48 Å
Translation7.74 Å51.48 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.8data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.26→29.944 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1928 5 %
Rwork0.2042 71498 -
obs0.206 38564 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.57 Å2 / Biso mean: 52.0792 Å2 / Biso min: 23.81 Å2
Refinement stepCycle: final / Resolution: 2.26→29.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 64 77 4428
Biso mean--40.6 44.58 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094480
X-RAY DIFFRACTIONf_angle_d1.1696083
X-RAY DIFFRACTIONf_chiral_restr0.044643
X-RAY DIFFRACTIONf_plane_restr0.006780
X-RAY DIFFRACTIONf_dihedral_angle_d14.7051659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.28860.38591350.33792667280298
2.2886-2.31880.3521480.324526242772100
2.3188-2.35050.30171330.304926342767100
2.3505-2.38410.32481100.286527042814100
2.3841-2.41960.35191340.277826882822100
2.4196-2.45740.31631470.252826202767100
2.4574-2.49770.27241480.25326772825100
2.4977-2.54070.23921200.252525882708100
2.5407-2.58690.28321350.235427022837100
2.5869-2.63670.29871170.236726612778100
2.6367-2.69040.32741590.22226812840100
2.6904-2.74890.30681290.233126012730100
2.7489-2.81280.28381210.211226932814100
2.8128-2.88310.24911350.200926512786100
2.8831-2.9610.25281540.193926122766100
2.961-3.0480.23311560.20126592815100
3.048-3.14630.23041490.192226332782100
3.1463-3.25860.24081450.206426452790100
3.2586-3.38890.23051510.197326672818100
3.3889-3.54290.22061360.196526682804100
3.5429-3.72940.21381330.188126582791100
3.7294-3.96260.25261570.17726242781100
3.9626-4.26770.24271610.184826452806100
4.2677-4.69570.22741390.175426212760100
4.6957-5.37180.2111400.18132632277299
5.3718-6.75510.20161400.20582613275398
6.7551-29.94680.17611320.1872630276299

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