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- PDB-6ay6: Naegleria fowleri CYP51-voriconazole complex -

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Basic information

Entry
Database: PDB / ID: 6ay6
TitleNaegleria fowleri CYP51-voriconazole complex
ComponentsCYP51, sterol 14alpha-demethylase
KeywordsOXIDOREDUCTASE / CYP51 / sterol 14alpha-demethylase
Function / homology
Function and homology information


steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding
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 / Voriconazole / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDebnath, A. / Calvet, C.M. / Jennings, G. / Zhou, W. / Aksenov, A. / Luth, M. / Abagyan, R. / Nes, W.D. / McKerrow, J.H. / Podust, L.M.
CitationJournal: PLoS Negl Trop Dis / Year: 2017
Title: CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM).
Authors: Debnath, A. / Calvet, C.M. / Jennings, G. / Zhou, W. / Aksenov, A. / Luth, M.R. / Abagyan, R. / Nes, W.D. / McKerrow, J.H. / Podust, L.M.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 27, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Oct 4, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYP51, sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5423
Polymers53,5761
Non-polymers9662
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: P450 (CYP) function as monomers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-24 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.180, 55.340, 73.220
Angle α, β, γ (deg.)90.000, 100.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CYP51, sterol 14alpha-demethylase


Mass: 53575.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Coding sequence synthetically generated
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: NF0102700 / Plasmid: pCW-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: A0A2H4A2U9*PLUS
#2: Chemical ChemComp-VOR / Voriconazole / (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 349.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F3N5O / Comment: medication, antifungal*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 33% PEG MME 550, 0.03 M CaCl2, 2% Jeffamine, 0.1 M bis-Tris propane, pH 7.1
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2017 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.4→71.92 Å / Num. obs: 18189 / % possible obs: 97.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.01
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 914 / % possible all: 66.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.462
Highest resolutionLowest resolution
Rotation71.93 Å3.2 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREP11.1.03phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TL8

5tl8


Resolution: 2.4→71.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 24.067 / SU ML: 0.282 / SU R Cruickshank DPI: 0.6381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.638 / ESU R Free: 0.33
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 933 5.1 %RANDOM
Rwork0.2187 ---
obs0.2222 17255 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.6 Å2 / Biso mean: 85.259 Å2 / Biso min: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å2-3.65 Å2
2---1.57 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 2.4→71.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 68 9 3660
Biso mean--62.39 76.78 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193738
X-RAY DIFFRACTIONr_bond_other_d0.0010.023605
X-RAY DIFFRACTIONr_angle_refined_deg1.0052.0085063
X-RAY DIFFRACTIONr_angle_other_deg0.57238309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1555448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95323.208159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61615670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71528
X-RAY DIFFRACTIONr_chiral_restr0.0540.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214118
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02832
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.548 43 -
Rwork0.461 867 -
all-910 -
obs--66.37 %
Refinement TLS params.Method: refined / Origin x: 18.4357 Å / Origin y: -0.1883 Å / Origin z: 19.1498 Å
111213212223313233
T0.138 Å20.0191 Å20.042 Å2-0.2152 Å2-0.0018 Å2--0.0755 Å2
L1.5844 °20.429 °20.3796 °2-2.7168 °20.0388 °2--1.7696 °2
S0.022 Å °0.0665 Å °-0.0852 Å °-0.2276 Å °-0.033 Å °0.0592 Å °-0.0149 Å °-0.0929 Å °0.0109 Å °

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