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- PDB-7rkt: Naegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(2,4-dichlor... -

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Basic information

Entry
Database: PDB / ID: 7rkt
TitleNaegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl 3-(trifluoromethyl)benzoate
ComponentsProtein CYP51
KeywordsOXIDOREDUCTASE / ergosterol biosynthesis / Azole inhibitors
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-5UR / PROTOPORPHYRIN IX CONTAINING FE / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSharma, V. / Podust, L.M.
CitationJournal: J.Med.Chem. / Year: 2023
Title: Miconazole-like Scaffold is a Promising Lead for Naegleria fowleri -Specific CYP51 Inhibitors.
Authors: Sharma, V. / Madia, V.N. / Tudino, V. / Nguyen, J.V. / Debnath, A. / Messore, A. / Ialongo, D. / Patacchini, E. / Palenca, I. / Basili Franzin, S. / Seguella, L. / Esposito, G. / Petrucci, R. ...Authors: Sharma, V. / Madia, V.N. / Tudino, V. / Nguyen, J.V. / Debnath, A. / Messore, A. / Ialongo, D. / Patacchini, E. / Palenca, I. / Basili Franzin, S. / Seguella, L. / Esposito, G. / Petrucci, R. / Di Matteo, P. / Bortolami, M. / Saccoliti, F. / Di Santo, R. / Scipione, L. / Costi, R. / Podust, L.M.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CYP51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7905
Polymers53,5601
Non-polymers1,2304
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.700, 55.190, 72.530
Angle α, β, γ (deg.)90.000, 100.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein CYP51


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
#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-5UR / (1S)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl 3-(trifluoromethyl)benzoate


Mass: 429.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H13Cl2F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.13 % / Description: Red elongated crystals of 0.3 mm size.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 mM Calcium chloride; 4.55% v/v Jefframine M-600 pH-7.0; 33% v/v Polyethylene glycol monomethyl ether 550; 100 mM Bis-Tris Propane pH-7.0

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Liquid Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.1→71.38 Å / Num. obs: 26825 / % possible obs: 96.1 % / Redundancy: 6.271 % / Biso Wilson estimate: 71.278 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.00092 / Rrim(I) all: 0.00101 / Χ2: 0.857 / Net I/σ(I): 9.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.3760.023850.5813440.1940.0277665.6
2.15-2.214.9420.023990.8417620.2890.026988
2.21-2.285.6820.020521.2618870.4650.0226397.5
2.28-2.356.7730.015941.9918800.7350.0172699.7
2.35-2.426.9180.01262.6618270.8030.0136299.8
2.42-2.516.8160.010013.5217720.8730.0108599.8
2.51-2.66.5210.007884.2917090.9170.0085699.8
2.6-2.716.6240.005765.8216450.9510.0062699.9
2.71-2.836.960.004087.5915810.9810.0044199.9
2.83-2.976.9280.002989.3714940.9850.0032299.9
2.97-3.136.6080.0020811.1414660.9870.0022699.9
3.13-3.326.510.0014713.6213670.9920.001699.8
3.32-3.556.90.0010816.8712700.9930.0011899.6
3.55-3.836.5760.0009118.6411900.9940.0009999.3
3.83-4.26.1050.0007520.3810980.9930.0008399.1
4.2-4.696.1760.0007421.8810000.9930.0008199.4
4.69-5.426.2220.0006922.298790.9950.0007598.5
5.42-6.645.7730.0007121.567350.9920.0007897.1
6.64-9.396.3650.000623.455910.9970.0006599
9.39-71.385.7470.0005422.53280.9970.000696.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TL8

5tl8


Resolution: 2.1→71.38 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 10.404 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1308 4.9 %RANDOM
Rwork0.1789 ---
obs0.1819 25517 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.02 Å2 / Biso mean: 79.644 Å2 / Biso min: 42.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å2-2.71 Å2
2---2.91 Å2-0 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 2.1→71.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 83 38 3739
Biso mean--66.78 74.1 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193798
X-RAY DIFFRACTIONr_bond_other_d0.0020.023674
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.0095138
X-RAY DIFFRACTIONr_angle_other_deg1.5693.0028471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47323.313163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95815687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3631528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214177
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02847
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.561 79 -
Rwork0.486 1261 -
obs--65.49 %

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