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

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Basic information

Entry
Database: PDB / ID: 3khm
TitleCrystal structure of sterol 14alpha-demethylase (CYP51) from Trypanosoma cruzi in complex with inhibitor fluconazole
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
Function / homology
Function and homology information


sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / 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-TPF / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 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)53,8483
Polymers52,9251
Non-polymers9232
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)62.591, 62.591, 222.248
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: 52925.340 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-481 / Mutation: F24K, N25T, T26S, T27G, R28K, P29G, T30K, D31L
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-TPF / 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL / FLUCONAZOLE / ALPHA-(2,4-DIFLUOROPHENYL)-ALPHA-(1H-1,2,4-TRIAZOLE-1-YLMETHYL)-1H-1,2,4-TRIAZOLE-1-ETHANOL / ELAZOR / TRIFLUCAN / BIOZOLENE


Mass: 306.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12F2N6O / Comment: medication*YM

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3350, POTASSIUM FORMATE, SODIUM CHLORIDE, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2005
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 12689 / Num. obs: 12181 / % possible obs: 96 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 3.6 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2136 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K1O

3k1o


Resolution: 2.85→28.83 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 46.601 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.4 / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27987 593 5.1 %RANDOM
Rwork0.22681 ---
obs0.22928 11141 94.17 %-
all-11830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 65 0 3582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223670
X-RAY DIFFRACTIONr_angle_refined_deg0.3652.0174969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.745438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.39223.292161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94115655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3071529
X-RAY DIFFRACTIONr_chiral_restr0.0250.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212758
X-RAY DIFFRACTIONr_mcbond_it0.7221.52204
X-RAY DIFFRACTIONr_mcangle_it1.39323569
X-RAY DIFFRACTIONr_scbond_it2.06931466
X-RAY DIFFRACTIONr_scangle_it3.3944.51400
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 39 -
Rwork0.351 664 -
obs--82.13 %
Refinement TLS params.Method: refined / Origin x: 9.732 Å / Origin y: -24.882 Å / Origin z: 18.256 Å
111213212223313233
T0.5813 Å20.1016 Å2-0.0074 Å2-0.2838 Å20.0258 Å2--0.2711 Å2
L3.6229 °20.3833 °20.0484 °2-4.2198 °20.9267 °2--4.5247 °2
S-0.2877 Å °0.3685 Å °-0.1357 Å °-0.5004 Å °0.0349 Å °0.0359 Å °-0.3608 Å °-0.5977 Å °0.2529 Å °

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