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- PDB-2wv2: X-ray structure of CYP51 from the human pathogen Trypanosoma bruc... -

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Basic information

Entry
Database: PDB / ID: 2wv2
TitleX-ray structure of CYP51 from the human pathogen Trypanosoma brucei in complex with fluconazole
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE
KeywordsOXIDOREDUCTASE / METHYLTRANSFERASE / P450 / IRON / CYP51 / METAL-BINDING / ERGOSTEROL BIOSYNTHESIS
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol metabolic process / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum
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 / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsChen, C.-K. / Leung, S.S.F. / Guilbert, C. / Jacobson, M. / McKerrow, J.H. / Podust, L.M.
CitationJournal: Plos Negl Trop Dis / Year: 2010
Title: Structural Characterization of Cyp51 from Trypanosoma Cruzi and Trypanosoma Brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole
Authors: Chen, C.-K. / Leung, S.S.F. / Guilbert, C. / Jacobson, M. / Mckerrow, J.H. / Podust, L.M.
History
DepositionOct 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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

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Assembly

Deposited unit
A: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8983
Polymers53,9761
Non-polymers9232
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.179, 106.179, 99.730
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 LANOSTEROL 14-ALPHA-DEMETHYLASE / STEROL 14 ALPHA-DEMETHYLASE / CYP51


Mass: 53975.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q385E8, sterol 14alpha-demethylase
#2: 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, antifungal*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 15% ETHYLENE GLYCOL 0-3% ACETONITRILE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587, 1.7393, 1.6531
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 19, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.73931
31.65311
ReflectionResolution: 2.7→92 Å / Num. obs: 18252 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 44 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 44 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
ELVESphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→92.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 28.442 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.274 920 5.1 %RANDOM
Rwork0.21 ---
obs0.213 17043 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å20 Å2
2---0.31 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 65 15 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223583
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9622.014877
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4295441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70923.245151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5815579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3391527
X-RAY DIFFRACTIONr_chiral_restr0.1120.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212734
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_it0.6531.52221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23823575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19631362
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5094.51302
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 61 -
Rwork0.538 1194 -
obs--95.58 %
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)
19.90820.66364.52675.951-3.090912.23460.25730.2218-0.5011-0.14140.60620.5230.4937-1.1865-0.86350.4060.12530.0750.41630.16130.2852-62.73116.727-10.944
21.9653-0.3678-0.01893.7044-0.97496.1494-0.046-0.4641-0.64221.04430.4191-1.07360.36880.1828-0.37310.7117-0.0606-0.31740.3236-0.08510.7381-35.7315.982.592
32.56570.6889-0.36963.7331-0.53384.81610.1914-0.7514-1.09020.74670.3198-0.43091.2406-0.6885-0.51111.012-0.1027-0.3110.60140.25690.6866-44.669-0.4577.651
48.0721-0.8515-0.21593.0690.176.21670.31670.09030.70070.03060.2689-0.647-1.3697-0.1456-0.58570.6986-0.020.16580.0498-0.07230.37-41.70721.491-9.119
57.2789-0.77760.02764.89011.59995.50190.35240.44650.2234-0.0730.3491-1.1729-0.84370.3424-0.70140.4615-0.12050.13480.1091-0.13890.4304-35.72315.971-11.245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 100
2X-RAY DIFFRACTION2A101 - 200
3X-RAY DIFFRACTION3A201 - 300
4X-RAY DIFFRACTION4A301 - 400
5X-RAY DIFFRACTION5A401 - 476

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