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

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Basic information

Entry
Database: PDB / ID: 5eaf
TitleSaccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor Fluquinconazole
ComponentsLanosterol 14-alpha demethylase
KeywordsOxidoreductase/Oxidoreducatse inhibitor / CYP51 / Fluquinconazole / 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-FQC / 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: 2.65 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 ...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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,7006
Polymers123,7142
Non-polymers1,9854
Water64936
1
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8503
Polymers61,8571
Non-polymers9932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8503
Polymers61,8571
Non-polymers9932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.560, 79.600, 81.130
Angle α, β, γ (deg.)99.960, 90.000, 90.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: HEM / End label comp-ID: HEM

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALchain AAA - C8 - 6018
2ILEILEchain BBB - E7 - 6017

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61857.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FQC is the small molecule Fluquinconazole
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FQC / 3-(2,4-dichlorophenyl)-6-fluoranyl-2-(1,2,4-triazol-1-yl)quinazolin-4-one / Fluquinconazole


Mass: 376.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H8Cl2FN5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6 / 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: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.65→29.899 Å / Num. obs: 43507 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Net I/σ(I): 6.8 / Num. measured all: 88236 / Scaling rejects: 37
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.65-2.780.6841.51141532380.8670.40898.9
8.79-61.540.05314.421356090.9930.03285.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.75 Å29.9 Å
Translation6.75 Å29.9 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.7data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.65→29.899 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 2118 4.86 %
Rwork0.2094 82680 -
obs0.2118 43507 89.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.2 Å2 / Biso mean: 59.329 Å2 / Biso min: 26.92 Å2
Refinement stepCycle: final / Resolution: 2.65→29.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8540 0 136 36 8712
Biso mean--45.55 49.16 -
Num. residues----1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018933
X-RAY DIFFRACTIONf_angle_d1.34512136
X-RAY DIFFRACTIONf_chiral_restr0.0541275
X-RAY DIFFRACTIONf_plane_restr0.0071593
X-RAY DIFFRACTIONf_dihedral_angle_d14.5533320
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5021X-RAY DIFFRACTION5.097TORSIONAL
12B5021X-RAY DIFFRACTION5.097TORSIONAL
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 (%)
2.65-2.68010.3631200.32342639275986
2.6801-2.71160.38841120.29992785289788
2.7116-2.74470.42421370.31532695283288
2.7447-2.77940.3597840.29412596268085
2.7794-2.81590.3221410.29892745288688
2.8159-2.85450.36051360.27032690282688
2.8545-2.89520.23871240.27722701282589
2.8952-2.93840.33481400.27642766290688
2.9384-2.98430.34261600.28472645280589
2.9843-3.03310.33661540.28182691284588
3.0331-3.08540.36141560.26462771292789
3.0854-3.14140.3141260.2592650277688
3.1414-3.20180.32451210.24772760288188
3.2018-3.26710.32861350.24662724285989
3.2671-3.3380.31911580.232682284088
3.338-3.41560.26371580.22862664282288
3.4156-3.50080.30311280.22532699282787
3.5008-3.59540.25911400.21252682282289
3.5954-3.7010.21461580.19562722288089
3.701-3.82020.23741480.20272802295091
3.8202-3.95640.23561800.19362891307194
3.9564-4.11450.24861800.19282792297294
4.1145-4.30120.24961600.18042878303894
4.3012-4.52720.22251380.16292960309894
4.5272-4.80980.20711520.1632866301895
4.8098-5.17940.18241460.17152952309895
5.1794-5.69740.25911200.18472916303695
5.6974-6.51440.24031380.18632934307295
6.5144-8.17950.18471560.1782872302894
8.1795-29.90040.23941200.1862510263082

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