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- PDB-6ayb: Naegleria fowleri CYP51-ketoconazole complex -

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Basic information

Entry
Database: PDB / ID: 6ayb
TitleNaegleria fowleri CYP51-ketoconazole 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 / Chem-KKK / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 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 8, 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 1.2Oct 4, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,0909
Polymers53,5921
Non-polymers1,4988
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-22 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.210, 55.250, 71.620
Angle α, β, γ (deg.)90.000, 100.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYP51, sterol 14alpha-demethylase


Mass: 53591.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS 371 and CYS 392 are spontaneously oxidized to sulfenic acid CSO
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Plasmid: pCW-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A2U9*PLUS

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Non-polymers , 5 types, 93 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-KKK / 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine


Mass: 531.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28Cl2N4O4 / Comment: medication, antifungal*YM
#6: 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 33% PEG MME 550, 0.03 CaCl2, 4% Jeffamine M-600, 0.1 M bis-Tris propane, pH 6.9
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: Sep 9, 2016 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.87→70.5 Å / Num. obs: 36286 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 6.07 % / Biso Wilson estimate: 42.85 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.223 / Χ2: 0.698 / Net I/σ(I): 3.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.87-1.924.7021.8870.5319130.3582.11868.4
1.92-1.975.0621.5710.7121600.3771.75278.9
1.97-2.035.5221.2481.0124420.5021.37592.5
2.03-2.096.5121.031.4325790.6781.12199.5
2.09-2.166.8470.8441.8324890.7870.915100
2.16-2.246.7220.6692.2924310.8460.72699.8
2.24-2.326.3990.5752.6323610.8570.62899.7
2.32-2.416.4160.4953.1322260.8660.54199.6
2.41-2.526.7130.4513.6221350.9070.49199
2.52-2.646.5480.3854.0820540.9410.42198.9
2.64-2.796.170.3124.6119360.9590.34299
2.79-2.966.010.2775.2818590.9530.30599.7
2.96-3.166.2450.2425.9917270.960.26598.4
3.16-3.415.9540.2056.7316230.9680.22698.7
3.41-3.745.4730.178715000.9660.19899
3.74-4.185.6420.1557.6413530.9780.17199
4.18-4.835.7520.1378.1212020.9840.15199
4.83-5.915.5160.1467.910290.9740.16199.7
5.91-8.366.0130.1378.447990.9780.1599
8.36-70.55.7590.1148.624680.9940.126100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.62 Å70.55 Å
Translation6.62 Å70.55 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TL8

5tl8


Resolution: 1.87→70.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.777 / SU ML: 0.191 / SU R Cruickshank DPI: 0.2047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1836 5.1 %RANDOM
Rwork0.2431 ---
obs0.2452 34450 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.94 Å2 / Biso mean: 46.123 Å2 / Biso min: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0 Å2-1.22 Å2
2--0.89 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.87→70.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 100 85 3712
Biso mean--41.98 44.39 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193710
X-RAY DIFFRACTIONr_bond_other_d0.0020.023518
X-RAY DIFFRACTIONr_angle_refined_deg1.262.015027
X-RAY DIFFRACTIONr_angle_other_deg0.65738094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73123.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214108
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02827
LS refinement shellResolution: 1.87→1.918 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 93 -
Rwork0.427 1818 -
all-1911 -
obs--68.35 %
Refinement TLS params.Method: refined / Origin x: 5.7941 Å / Origin y: 25.6368 Å / Origin z: 89.0848 Å
111213212223313233
T0.1149 Å20.0222 Å2-0.0037 Å2-0.0505 Å2-0.0018 Å2--0.0623 Å2
L0.742 °20.1299 °20.1341 °2-1.4877 °20.13 °2--1.692 °2
S0.0249 Å °-0.0016 Å °-0.0582 Å °0.0147 Å °-0.0201 Å °0.0749 Å °0.0281 Å °-0.2725 Å °-0.0048 Å °

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