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- PDB-6ay4: Naegleria fowleri CYP51-fluconazole complex -

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Basic information

Entry
Database: PDB / ID: 6ay4
TitleNaegleria fowleri CYP51-fluconazole complex
ComponentsCYP51, sterol 14alpha-demethylase
KeywordsOXIDOREDUCTASE / CYP51 / sterol 14alpha-demethylase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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 / Chem-TPF / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CYP51, sterol 14alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7317
Polymers53,5601
Non-polymers1,1716
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: P450 (CYP) are monomeric proteins
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-7 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.110, 55.310, 73.490
Angle α, β, γ (deg.)90.000, 101.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CYP51, sterol 14alpha-demethylase


Mass: 53559.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TPF / 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL / FLUCONAZOLE / ALPHA-(2,4-DIFLUOROPHENYL)-ALPHA-(1H-1,2,4-TRIAZOLE-1-YLMETHYL)-1H-1,2,4-TRIAZOLE-1-ETHANOL / ELAZOR / TRIFLUCAN / BIOZOLENE


Mass: 306.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12F2N6O / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 33% PEG MME 550, 0.03 M CaCl2, 4% 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: Liquid 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: 2.7→72.01 Å / Num. obs: 13108 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.584 % / Biso Wilson estimate: 85.618 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.087 / Χ2: 0.974 / Net I/σ(I): 7.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.772.6081.6040.579760.4271.99199.8
2.77-2.852.611.310.749210.5361.62698.2
2.85-2.932.4340.9780.99330.6111.23598.5
2.93-3.022.6450.8071.218890.675199.6
3.02-3.122.7370.6511.628510.7470.897.6
3.12-3.232.710.4592.318510.8820.56697.9
3.23-3.352.6170.3422.958090.930.42299.1
3.35-3.492.4830.2454.027720.9670.30497
3.49-3.642.420.1745.147310.9820.21998.1
3.64-3.822.650.1168.127170.9870.14298
3.82-4.022.640.0879.876750.9930.10796.3
4.02-4.272.6360.05213.256450.9970.06498.5
4.27-4.562.4720.04515.566020.9980.05697.9
4.56-4.932.4930.03817.175680.9980.04897.6
4.93-5.42.6870.03718.25150.9980.04697
5.4-6.042.6590.04118.724750.9970.05197.1
6.04-6.972.3980.03519.914020.9970.04494.1
6.97-8.542.5790.02726.643490.9980.03396.4
8.54-12.072.5530.02329.882730.9980.02993.5
12.07-72.012.370.02529.311540.9980.03290.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.501
Highest resolutionLowest resolution
Rotation72.01 Å3.35 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 / Resolution: 2.7→72.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 54.086 / SU ML: 0.531 / SU R Cruickshank DPI: 0.4247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3132 665 5.1 %RANDOM
Rwork0.2569 ---
obs0.2598 12443 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.86 Å2 / Biso mean: 97.763 Å2 / Biso min: 45.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å2-7.49 Å2
2---4.24 Å20 Å2
3---4.65 Å2
Refinement stepCycle: final / Resolution: 2.7→72.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 81 5 3670
Biso mean--93.04 93.3 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193748
X-RAY DIFFRACTIONr_bond_other_d00.023618
X-RAY DIFFRACTIONr_angle_refined_deg1.5062.0075069
X-RAY DIFFRACTIONr_angle_other_deg0.64138336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.775449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63423.208159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17715668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4851528
X-RAY DIFFRACTIONr_chiral_restr0.060.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214122
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02829
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 62 -
Rwork0.364 913 -
all-975 -
obs--99.09 %
Refinement TLS params.Method: refined / Origin x: 18.5192 Å / Origin y: 0.0565 Å / Origin z: 19.1614 Å
111213212223313233
T0.3112 Å20.0051 Å20.2578 Å2-0.5589 Å2-0.0024 Å2--0.2343 Å2
L1.8663 °20.3036 °20.6414 °2-3.269 °2-0.0174 °2--1.223 °2
S-0.0353 Å °0.1306 Å °-0.0436 Å °0.1161 Å °0.0458 Å °-0.159 Å °-0.0437 Å °-0.1005 Å °-0.0104 Å °

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