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- PDB-3k1o: Crystal structure of sterol 14-alpha demethylase (CYP51) from Try... -

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Basic information

Entry
Database: PDB / ID: 3k1o
TitleCrystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in complex with a potential antichagasic drug, posaconazole
ComponentsSterol 14 alpha-demethylase
KeywordsOXIDOREDUCTASE / sterol 14-alpha demethylase / eburicol 14a-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 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / 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-POZ / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
DepositionSep 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 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 1.5Sep 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)53,6703
Polymers52,3531
Non-polymers1,3172
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.121, 63.121, 229.302
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-POZ / 2,5-anhydro-1,3,4-trideoxy-2-(2,4-difluorophenyl)-6-O-{4-[4-(4-{1-[(1S,2S)-1-ethyl-2-hydroxypropyl]-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl}phenyl)piperazin-1-yl]phenyl}-1-(1H-1,2,4-triazol-1-yl)-D-erythro-hexitol


Mass: 700.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H42F2N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
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: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.89→30 Å / Num. all: 11966 / Num. obs: 11910 / % possible obs: 99.53 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 4.1 / Redundancy: 8.5 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26
Reflection shellResolution: 2.89→2.94 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3G1Q

3g1q


Resolution: 2.89→29.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 37.9 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 4.1 / σ(I): 4.1 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27597 606 4.8 %RANDOM
Rwork0.22807 ---
obs0.23033 11910 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.997 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.14 Å20 Å2
2---0.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.89→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 94 10 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223681
X-RAY DIFFRACTIONr_angle_refined_deg1.6972.0224993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.835439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.71823.354158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4011527
X-RAY DIFFRACTIONr_chiral_restr0.0540.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212776
X-RAY DIFFRACTIONr_mcbond_it0.771.52210
X-RAY DIFFRACTIONr_mcangle_it1.48123571
X-RAY DIFFRACTIONr_scbond_it2.44131471
X-RAY DIFFRACTIONr_scangle_it4.0784.51422
LS refinement shellResolution: 2.89→2.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 43 -
Rwork0.295 836 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1505-0.19251.64412.2239-0.05074.9709-0.0632-0.05730.33070.4274-0.21560.0404-0.6487-0.87940.27890.3943-0.11440.05110.5155-0.09340.1052-42.5686.462-20.679
22.1153-0.04360.09134.88091.74583.90470.0075-0.15730.4409-0.1249-0.0558-0.1846-0.5047-0.03080.04840.488-0.258-0.17480.58380.0660.2559-27.50115.934-9.437
32.95080.2611.01981.97450.24813.5519-0.006-0.0041-0.14160.2873-0.1252-0.1734-0.0361-0.11940.13120.2867-0.18740.02090.40640.04920.1644-32.405-0.964-21.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 161
2X-RAY DIFFRACTION2A162 - 260
3X-RAY DIFFRACTION3A261 - 477

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