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- PDB-3zg2: Sterol 14 alpha-demethylase (CYP51) from Trypanosoma cruzi in com... -

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Basic information

Entry
Database: PDB / ID: 3zg2
TitleSterol 14 alpha-demethylase (CYP51) from Trypanosoma cruzi in complex with the pyridine inhibitor (S)-2-(4-chlorophenyl)-2-(pyridin-3-yl)-1- (4-(4-(trifluoromethyl)phenyl)piperazin-1-yl)ethanone (EPL-BS1246,UDO)
ComponentsSTEROL 14-ALPHA DEMETHYLASE
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / STEROL BIOSYNTHESIS / EUKARYOTIC MEMBRANES / CYTOCHROME P450 FOLD / ENDOPLASMIC RETICULUM MEMBRANE / INHIBITOR
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-UDO / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Keenan, M. / Chatelain, E. / Lepesheva, G.I.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Complexes of Trypanosoma Cruzi Sterol 14Alpha-Demethylase (Cyp51) with Two Pyridine-Based Drug Candidates for Chagas Disease: Structural Basis for Pathogen-Selectivity
Authors: Hargrove, T.Y. / Wawrzak, Z. / Alexander, P.W. / Chaplin, J.H. / Keenan, M. / Charman, S.A. / Perez, C.J. / Waterman, M.R. / Chatelain, E. / Lepesheva, G.I.
History
DepositionDec 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6293
Polymers52,5531
Non-polymers1,0762
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.699, 63.699, 223.263
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 / CYP51 / TC14DM / CYTOCHROME P450 51


Mass: 52552.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-481 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: THLAHUEN / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / References: UniProt: Q7Z1V1, 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-UDO / (S)-2-(4-chlorophenyl)-2-pyridin-3-yl-1-[4-[4-(trifluoromethyl)phenyl]piperazin-1-yl]ethanone


Mass: 459.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21ClF3N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN LEPESHEVA ET AL. (2006) J. BIOL.CHEM., 281, P.3577

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MAGNESIUM CHLORIDE, POTASSIUM PHOSPHATE, GLYCEROL, PEG 3500, CYMAL 4, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2012 / Details: BE LENSES DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 13689 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 21.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 69.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K1O

3k1o


Resolution: 2.8→27.66 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.837 / SU B: 44.953 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28245 651 5.3 %RANDOM
Rwork0.26841 ---
obs0.26911 12182 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.85 Å20 Å2
2--0.85 Å20 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 75 13 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0193757
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9935092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2423.452168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.9115663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5941529
X-RAY DIFFRACTIONr_chiral_restr0.0970.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212847
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.804→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 27 -
Rwork0.322 461 -
obs--51.05 %
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)
14.79210.2629-1.15443.6143-0.30382.3398-0.23560.89120.0238-0.3449-0.0255-0.39120.2207-0.15960.26110.2179-0.1968-0.02510.3490.0420.244117.479420.8902-18.9897
22.36330.49411.20442.60550.27080.7545-0.79240.222-0.0943-0.42470.8884-0.2902-0.4762-0.0913-0.0960.3322-0.0690.09730.63940.09620.293217.537225.6603-18.0104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 1490
2X-RAY DIFFRACTION2A2001 - 2013

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