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- PDB-7rkr: Naegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(4-fluorophe... -

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Basic information

Entry
Database: PDB / ID: 7rkr
TitleNaegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(4-fluorophenyl)-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
PROTOPORPHYRIN IX CONTAINING FE / Chem-L49 / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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

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Assembly

Deposited unit
A: Protein CYP51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6355
Polymers53,5601
Non-polymers1,0754
Water1,78399
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)120.860, 55.350, 71.490
Angle α, β, γ (deg.)90.000, 100.120, 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-L49 / (1S)-1-(4-fluorophenyl)-2-(1H-imidazol-1-yl)ethyl 3-(trifluoromethyl)benzoate


Mass: 378.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14F4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.2 Å3/Da / Density % sol: 44.13 % / 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; 4.50% 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: Mar 6, 2020 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.76→70.38 Å / Num. obs: 45818 / % possible obs: 98.1 % / Redundancy: 6.421 % / Biso Wilson estimate: 46.872 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.00096 / Rrim(I) all: 0.00104 / Χ2: 0.834 / Net I/σ(I): 8.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.76-1.84.2220.045140.3626780.1490.0509977.7
1.8-1.856.4070.030540.733420.4190.0332499.9
1.85-1.96.7750.025660.9332510.4930.0277999.8
1.9-1.966.7240.017171.4531290.6420.01862100
1.96-2.036.560.01208230580.7540.0131399.8
2.03-2.16.2710.008882.7429840.8240.009799.9
2.1-2.186.8580.006833.8728580.8940.0074100
2.18-2.276.6760.005554.9827250.920.0060399.5
2.27-2.376.710.003966.4526450.9610.004399.7
2.37-2.486.3930.003087.6425410.9740.0033699.9
2.48-2.626.6650.002389.6924030.9830.00259100
2.62-2.786.9170.0015912.4523110.9920.0017299.9
2.78-2.976.830.0012115.121230.9950.00131100
2.97-3.26.3210.0009717.5920200.9950.0010699.8
3.2-3.516.5550.0007522.6218350.9960.0008299.8
3.51-3.926.5050.0006226.0416820.9960.0006799.7
3.92-4.535.9680.0005527.0914560.9970.0006199
4.53-5.556.0740.0005128.0312510.9970.0005698.4
5.55-7.856.1940.000528.449680.9980.0005499
7.85-70.385.9950.0003629.575580.9990.0003998.1

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Processing

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

5tl8


Resolution: 1.76→70.38 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.284 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 2308 5 %RANDOM
Rwork0.1878 ---
obs0.1904 43404 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.52 Å2 / Biso mean: 48.165 Å2 / Biso min: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å2-0 Å2-1.03 Å2
2---0.43 Å20 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 1.76→70.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 72 99 3779
Biso mean--36.51 49.62 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193765
X-RAY DIFFRACTIONr_bond_other_d0.0020.023637
X-RAY DIFFRACTIONr_angle_refined_deg1.7752.0075096
X-RAY DIFFRACTIONr_angle_other_deg1.04638386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50623.333162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05615681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861528
X-RAY DIFFRACTIONr_chiral_restr0.1140.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214147
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02842
LS refinement shellResolution: 1.76→1.801 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.549 112 -
Rwork0.538 2451 -
obs--74.51 %

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