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- PDB-3ksw: Crystal structure of sterol 14alpha-demethylase (CYP51) from Tryp... -

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Basic information

Entry
Database: PDB / ID: 3ksw
TitleCrystal structure of sterol 14alpha-demethylase (CYP51) from Trypanosoma cruzi in complex with an inhibitor VNF ((4-(4-chlorophenyl)-N-[2-(1H-imidazol-1-yl)-1-phenylethyl]benzamide)
ComponentsSterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / STEROL 14-ALPHA DEMETHYLASE / CYP51 / CYTOCHROME P450 / HEME / MONOOXYGENASE / ENDOPLASMIC RETICULUM / TRANSMEMBRANE PROTEIN / STEROL BIOSYNTHESIS / LIPIDS / MEMBRANE / IRON / HEME THIOLATE PROTEIN / Lipid synthesis / Metal-binding / NADP / Steroid biosynthesis
Function / homology
Function and homology information


steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding / membrane
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-VNF / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLepesheva, G.I. / Hargrove, T.Y. / Anderson, S. / Wawrzak, Z. / Waterman, M.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insights into Inhibition of Sterol 14{alpha}-Demethylase in the Human Pathogen Trypanosoma cruzi.
Authors: Lepesheva, G.I. / Hargrove, T.Y. / Anderson, S. / Kleshchenko, Y. / Furtak, V. / Wawrzak, Z. / Villalta, F. / Waterman, M.R.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3713
Polymers52,3531
Non-polymers1,0182
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.468, 66.468, 234.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sterol 14-alpha demethylase


Mass: 52352.645 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-481 / Mutation: T30K, D31T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: CYP51 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#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-VNF / 4'-chloro-N-[(1R)-2-(1H-imidazol-1-yl)-1-phenylethyl]biphenyl-4-carboxamide


Mass: 401.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20ClN3O

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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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, SODIUM FORMATE, SODIUM CHLORIDE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.05391 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2006
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05391 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 13424 / Num. obs: 12216 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.1
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique all: 412 / % possible all: 43.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3k1o

3k1o


Resolution: 3.05→28.57 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 54.663 / SU ML: 0.512 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29246 519 4.7 %RANDOM
Rwork0.24487 ---
obs0.24693 10505 90.96 %-
all-11544 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 3.05→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 72 0 3586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223678
X-RAY DIFFRACTIONr_angle_refined_deg0.622.0134988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7765442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.44323.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50415636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3211527
X-RAY DIFFRACTIONr_chiral_restr0.0440.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212790
X-RAY DIFFRACTIONr_mcbond_it0.821.52222
X-RAY DIFFRACTIONr_mcangle_it1.58823596
X-RAY DIFFRACTIONr_scbond_it2.40431456
X-RAY DIFFRACTIONr_scangle_it4.2654.51392
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 17 -
Rwork0.445 415 -
obs--49.77 %
Refinement TLS params.Method: refined / Origin x: 10.319 Å / Origin y: 26.661 Å / Origin z: 20.008 Å
111213212223313233
T1.3375 Å2-0.1525 Å2-0.0678 Å2-0.8096 Å20.0038 Å2--0.8559 Å2
L2.8596 °2-0.1138 °20.1339 °2-4.687 °20.8493 °2--7.6662 °2
S-0.556 Å °-0.3062 Å °0.3724 Å °0.7902 Å °0.1664 Å °-0.2005 Å °0.5967 Å °-0.9598 Å °0.3896 Å °

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