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- PDB-2wx2: X-RAY STRUCTURE OF CYP51 FROM THE HUMAN PATHOGEN TRYPANOSOMA CRUZ... -

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Basic information

Entry
Database: PDB / ID: 2wx2
TitleX-RAY STRUCTURE OF CYP51 FROM THE HUMAN PATHOGEN TRYPANOSOMA CRUZI IN COMPLEX WITH FLUCONAZOLE
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE
KeywordsOXIDOREDUCTASE / P450 / HEME / IRON / METAL-BINDING / METHYLTRANSFERASE / ERGOSTEROL BIOSYNTHESIS
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-TPF / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 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: LANOSTEROL 14-ALPHA-DEMETHYLASE
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0876
Polymers108,2422
Non-polymers1,8464
Water7,728429
1
A: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0443
Polymers54,1211
Non-polymers9232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0443
Polymers54,1211
Non-polymers9232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.993, 101.472, 74.729
Angle α, β, γ (deg.)90.00, 111.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.53951, -0.27526, 0.79571), (-0.25467, -0.95413, -0.15739), (0.80254, -0.11772, -0.58487)
Vector: 16.46348, 49.28086, -0.10636)

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Components

#1: Protein LANOSTEROL 14-ALPHA-DEMETHYLASE / CYP51


Mass: 54120.766 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-481
Source method: isolated from a genetically manipulated source
Details: FIRST 20 RESIDUES UPSTREAM OF K21 WERE REPLACED WITH THE FRAGMENT MAKKKKK
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q7Z1V1, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / 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 / Fluconazole


Mass: 306.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12F2N6O / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME IRON AND CYS 422 FLUCONAZOLE ...PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME IRON AND CYS 422 FLUCONAZOLE (TPF): COORDINATION BOND TO THE HEME IRON
Sequence detailsTHE FIRST 21 RESIDUES UPSTREAM OF K22 WERE REPLACED WITH THE FRAGMENT MAKKKKK AT THE N-TERMINUS. ...THE FIRST 21 RESIDUES UPSTREAM OF K22 WERE REPLACED WITH THE FRAGMENT MAKKKKK AT THE N-TERMINUS. HIS6-TAG WAS INTRODUCED AT THE C-TERMINUS

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 4000, 0.1 M BIS-TRIS, PH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.27→24.3 Å / Num. obs: 40051 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 55.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUZ

2wuz


Resolution: 2.27→69.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.872 / SU B: 18.013 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.27339 1944 4.9 %RANDOM
Rwork0.19277 ---
obs0.19677 38067 89.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.91 Å2
2---0.05 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.27→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6943 0 130 429 7502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7362.0099895
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90223.28314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.953151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5361553
X-RAY DIFFRACTIONr_chiral_restr0.1170.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215543
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_it0.8511.54438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46327170
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32632835
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.564.52725
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.48337273
X-RAY DIFFRACTIONr_sphericity_free6.5763430
X-RAY DIFFRACTIONr_sphericity_bonded2.30837084
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 81 -
Rwork0.203 1604 -
obs--50.78 %

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