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- PDB-5fsa: Crystal structure of sterol 14-alpha demethylase (CYP51) from a p... -

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Basic information

Entry
Database: PDB / ID: 5fsa
TitleCrystal structure of sterol 14-alpha demethylase (CYP51) from a pathogenic yeast Candida albicans in complex with the antifungal drug posaconazole
ComponentsCYP51 VARIANT1
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / HEME / MONOOXYGENASE / STEROL BIOSYNTHESIS / EUKARYOTIC MEMBRANES / CYTOCHROME P450 FOLD / ENDOPLASMIC RETICULUM MEMBRANE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cell growth mode switching, budding to filamentous / membrane raft polarization / ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity ...cell growth mode switching, budding to filamentous / membrane raft polarization / ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane / plasma 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 / POSACONAZOLE / Lanosterol 14-alpha demethylase / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Friggeri, L. / Lepesheva, G.I.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of Candida albicans sterol 14 alpha-demethylase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis.
Authors: Hargrove, T.Y. / Friggeri, L. / Wawrzak, Z. / Qi, A. / Hoekstra, W.J. / Schotzinger, R.J. / York, J.D. / Guengerich, F.P. / Lepesheva, G.I.
History
DepositionJan 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYP51 VARIANT1
B: CYP51 VARIANT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5056
Polymers112,8702
Non-polymers2,6354
Water2,288127
1
A: CYP51 VARIANT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7523
Polymers56,4351
Non-polymers1,3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYP51 VARIANT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7523
Polymers56,4351
Non-polymers1,3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.590, 72.910, 79.710
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CYP51 VARIANT1 / STEROL 14ALPHA-DEMETHYLASE


Mass: 56435.188 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 49-528 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HMS-174
References: UniProt: Q9P4W0, UniProt: P10613*PLUS, sterol 14alpha-demethylase
#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-X2N / POSACONAZOLE


Mass: 700.777 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H42F2N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.33 Å3/Da / Density % sol: 47.23 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 6, 2015 / Details: BE LENSES DIAMOND LAUE
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.86→50.39 Å / Num. obs: 23728 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.86→2.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.18 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UYL

4uyl


Resolution: 2.86→50.39 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.905 / SU B: 21.67 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25612 1224 5.2 %RANDOM
Rwork0.24056 ---
obs0.24138 22504 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.447 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å20.28 Å2
2---0.87 Å20 Å2
3----4.58 Å2
Refinement stepCycle: LAST / Resolution: 2.86→50.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 188 127 8163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0198284
X-RAY DIFFRACTIONr_bond_other_d0.0050.027704
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.98711265
X-RAY DIFFRACTIONr_angle_other_deg0.682317772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95823.545378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.416151373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4481546
X-RAY DIFFRACTIONr_chiral_restr0.0870.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219223
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4227.2023866
X-RAY DIFFRACTIONr_mcbond_other5.3987.1983865
X-RAY DIFFRACTIONr_mcangle_it8.82110.7884829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7817.4794415
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 88 -
Rwork0.302 1650 -
obs--99.66 %

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