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- PDB-6ayc: Naegleria fowleri CYP51-itraconazole complex -

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Basic information

Entry
Database: PDB / ID: 6ayc
TitleNaegleria fowleri CYP51-itraconazole complex
ComponentsProtein CYP51
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
Chem-1YN / PROTOPORPHYRIN IX CONTAINING FE / CYP51, sterol 14alpha-demethylase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Feb 21, 2018Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Oct 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

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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)54,8823
Polymers53,5601
Non-polymers1,3222
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-24 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.300, 55.190, 72.390
Angle α, β, γ (deg.)90.000, 100.620, 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) / 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-1YN / 2-[(2R)-butan-2-yl]-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one / Itraconazole


Mass: 705.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38Cl2N8O4 / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 33% PEG MME 550, 0.03 M CaCl2, 3% Jeffamine M-600, 0.1 M bis-Tris propane, pH 7.5
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
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.6→71.15 Å / Num. obs: 14541 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.535 % / Biso Wilson estimate: 85.962 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.146 / Χ2: 1.082 / Net I/σ(I): 7.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.676.8742.8650.5910690.3033.199.8
2.67-2.746.8282.3670.7510500.4242.564100
2.74-2.826.6521.6511.089910.6061.792100
2.82-2.916.4161.4221.2710090.6541.55199.8
2.91-36.7031.0521.759500.8221.141100
3-3.117.0210.8732.199190.8920.94399.7
3.11-3.236.8130.5483.318860.9360.59499.7
3.23-3.366.6730.3874.318510.9770.42199.8
3.36-3.516.3110.3075.58370.9820.33699.9
3.51-3.686.360.2266.998030.9860.24799.8
3.68-3.886.5830.1649.737360.9930.17899.5
3.88-4.116.4420.13311.927040.9920.14598.7
4.11-4.396.180.10713.726720.9940.117100
4.39-4.755.7810.09415.26110.9950.10497.9
4.75-5.26.4470.09116.795750.9940.199.8
5.2-5.816.5120.09716.75200.9930.10599.4
5.81-6.716.1110.08817.154700.9930.09798.7
6.71-8.226.2180.06820.384000.9970.075100
8.22-11.636.2770.0622.523070.9950.06699.7
11.63-71.155.9060.05522.051810.9940.06198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.475
Highest resolutionLowest resolution
Rotation71.15 Å3.29 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: 2.6→71.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 46.561 / SU ML: 0.421 / SU R Cruickshank DPI: 0.3446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.399
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 724 5 %RANDOM
Rwork0.2183 ---
obs0.2217 13816 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.69 Å2 / Biso mean: 95.087 Å2 / Biso min: 56.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-6.13 Å2
2--1.65 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: final / Resolution: 2.6→71.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 141 13 3731
Biso mean--86.87 72.64 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193815
X-RAY DIFFRACTIONr_bond_other_d0.0010.023656
X-RAY DIFFRACTIONr_angle_refined_deg1.9382.035176
X-RAY DIFFRACTIONr_angle_other_deg0.92138424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60223.208159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29215666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.241528
X-RAY DIFFRACTIONr_chiral_restr0.1090.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02849
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 60 -
Rwork0.619 1003 -
all-1063 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 18.461 Å / Origin y: -0.2284 Å / Origin z: 18.881 Å
111213212223313233
T0.2252 Å20.0408 Å2-0.0384 Å2-0.1692 Å20.0048 Å2--0.0262 Å2
L2.032 °20.5718 °20.8966 °2-3.1935 °20.2761 °2--1.9072 °2
S0.0994 Å °0.0801 Å °-0.0772 Å °-0.0808 Å °-0.0551 Å °-0.0346 Å °-0.0004 Å °-0.1337 Å °-0.0443 Å °

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