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- PDB-5jlc: Structure of CYP51 from the pathogen Candida glabrata -

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Basic information

Entry
Database: PDB / ID: 5jlc
TitleStructure of CYP51 from the pathogen Candida glabrata
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCATSE INHIBITOR / pathogen / Candida glabrata / CYP51 / itraconazole / OXIDOREDUCTASE-OXIDOREDUCATSE INHIBITOR complex
Function / homology
Function and homology information


ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / 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-1YN / PROTOPORPHYRIN IX CONTAINING FE / TRIETHYLENE GLYCOL / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKeniya, M.V. / Sabherwal, M. / Wilson, R.K. / Sagatova, A.A. / 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: Antimicrob.Agents Chemother. / Year: 2018
Title: Crystal Structures of Full-Length Lanosterol 14 alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery.
Authors: Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Woods, M.A. / Sagatova, A.A. / Tyndall, J.D.A. / 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.
#2: 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.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Feb 12, 2020Group: Database references / Polymer sequence / Category: citation / citation_author / entity_poly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.pdbx_target_identifier
Revision 2.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1097
Polymers59,3281
Non-polymers1,7816
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)237.940, 237.940, 237.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lanosterol 14-alpha demethylase / CYPLI / Cytochrome P450 51 / Cytochrome P450-14DM / Cytochrome P450-LIA1 / Sterol 14-alpha demethylase


Mass: 59327.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: ERG11, CYP51, CAGL0E04334g / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ADdelta / References: UniProt: P50859, sterol 14alpha-demethylase

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Non-polymers , 6 types, 91 molecules

#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-1YN / 2-[(2R)-butan-2-yl]-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one / Itraconazole


Mass: 705.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38Cl2N8O4 / Comment: medication, antifungal*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 4.73 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.5 M Glycine,40% PEG400

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.4→97.14 Å / Num. obs: 44748 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 43.44 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.496.11.5521100
8.98-97.145.60.072198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.82 Å97.14 Å
Translation7.82 Å97.14 Å

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHASER2.5.6phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 2.4→48.569 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.49
RfactorNum. reflection% reflection
Rfree0.231 4221 4.97 %
Rwork0.2005 --
obs0.202 44748 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.18 Å2 / Biso mean: 47.9072 Å2 / Biso min: 24.88 Å2
Refinement stepCycle: final / Resolution: 2.4→48.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 120 85 4334
Biso mean--64.92 46.28 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084385
X-RAY DIFFRACTIONf_angle_d0.9865948
X-RAY DIFFRACTIONf_chiral_restr0.061617
X-RAY DIFFRACTIONf_plane_restr0.006787
X-RAY DIFFRACTIONf_dihedral_angle_d11.8772619
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 (%)
2.4004-2.42760.37541290.327727122841100
2.4276-2.45620.35121380.328627072845100
2.4562-2.48620.37341440.320326842828100
2.4862-2.51760.34281570.313626632820100
2.5176-2.55080.38071480.296627052853100
2.5508-2.58570.2911360.291426752811100
2.5857-2.62260.2641470.276226682815100
2.6226-2.66180.29171330.267127182851100
2.6618-2.70340.26711360.262527202856100
2.7034-2.74770.28991500.251426722822100
2.7477-2.79510.29971480.242426842832100
2.7951-2.84590.29821520.231726552807100
2.8459-2.90060.26011380.230627522890100
2.9006-2.95980.26541470.215426422789100
2.9598-3.02420.21491260.219227062832100
3.0242-3.09450.26231540.214326772831100
3.0945-3.17190.23961400.205827152855100
3.1719-3.25760.28891420.193926692811100
3.2576-3.35340.21091310.185226912822100
3.3534-3.46170.18891680.181126852853100
3.4617-3.58530.22561160.178827302846100
3.5853-3.72880.15451250.170827002825100
3.7288-3.89850.19281060.157627422848100
3.8985-4.10390.18781320.158527152847100
4.1039-4.36090.18811600.171326522812100
4.3609-4.69730.18061340.155227012835100
4.6973-5.16960.18661610.166926662827100
5.1696-5.91650.2121130.18672703281699
5.9165-7.44980.23941580.20442661281999
7.4498-48.57920.24591520.20342639279198

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