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- PDB-2wuz: X-ray structure of CYP51 from Trypanosoma cruzi in complex with f... -

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Basic information

Entry
Database: PDB / ID: 2wuz
TitleX-ray structure of CYP51 from Trypanosoma cruzi in complex with fluconazole in alternative conformation
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE
KeywordsOXIDOREDUCTASE / METHYLTRANSFERASE / P450 / IRON / CYP51 / METAL-BINDING / ERGOSTEROL BIOSYNTHESIS
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: 2.35 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 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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, PUTATIVE
B: LANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0876
Polymers108,2422
Non-polymers1,8464
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-64.1 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.858, 92.574, 78.277
Angle α, β, γ (deg.)90.00, 102.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 30 - 475 / Label seq-ID: 16 - 461

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.99986, 0.00118, 0.01678), (-0.00103, -0.99996, 0.00896), (0.01679, 0.00894, 0.99982)
Vector: 37.33375, -15.76784, -0.36569)

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Components

#1: Protein LANOSTEROL 14-ALPHA-DEMETHYLASE, PUTATIVE / STEROL 14 ALPHA-DEMETHYLASE / CYP51


Mass: 54120.766 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
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.: 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


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME FE AND CYS422 FLUCONAZOLE ...PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN THE HEME FE AND CYS422 FLUCONAZOLE (TPF): COORDINATION BOND BETWEEN THE HEME FE AND FLUCONAZOLE
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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6 / Details: 40% POLYPROPYLENE GLYCOL 400, 0.1 TRIS-HCL, PH=6.0

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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: Aug 21, 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: 2.35→76.5 Å / Num. obs: 40838 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 70.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WV2

2wv2


Resolution: 2.35→76.53 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.542 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. SIDE CHAINS NOT VISIBLE IN THE DENSITY WAS MODELED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.27476 2046 5 %RANDOM
Rwork0.21739 ---
obs0.22028 38792 93.63 %-
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: 44.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.48 Å2
2---1.32 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.35→76.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 130 176 7265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8912.019948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51523.183311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.932151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1711555
X-RAY DIFFRACTIONr_chiral_restr0.1140.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215564
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_it0.8411.54472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4527224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32432842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5234.52724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.53437314
X-RAY DIFFRACTIONr_sphericity_free8.2883179
X-RAY DIFFRACTIONr_sphericity_bonded2.12837124
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1684tight positional0.060.05
2B1684tight positional0.060.05
1A1628medium positional0.10.5
2B1628medium positional0.10.5
1A1684tight thermal0.10.5
2B1684tight thermal0.10.5
1A1628medium thermal0.12
2B1628medium thermal0.12
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 99 -
Rwork0.244 1964 -
obs--64.01 %
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)
10.7008-0.3741-0.29242.5695-0.71.18140.0494-0.08640.05140.5103-0.1049-0.22110.0030.21420.05560.1901-0.0044-0.04930.10110.05090.094339.017-21.72116.287
20.9391-0.70140.18412.0865-0.31331.62210.13-0.0112-0.22990.0891-0.13270.02040.16930.11350.00270.09020.0299-0.02020.06310.04810.095633.498-28.1978.555
30.4559-0.11790.36432.10160.35781.29990.0034-0.06340.02870.4076-0.04680.2513-0.0688-0.34610.04340.11120.03230.05340.1328-0.03290.1065-1.3196.36816.412
41.0693-0.50620.60491.89530.18352.37390.1080.04280.23040.1169-0.04750.0036-0.16-0.1828-0.06060.07770.04770.04270.0633-0.01230.13343.96212.4359.224
51.1423-0.19390.31332.97120.43231.9550.13140.28820.0865-0.4125-0.2628-0.1849-0.02620.27370.13150.07910.07680.05290.13910.06550.104136.499-18.283-2.165
60.7663-0.17970.0351.7608-0.26071.0657-0.0011-0.18030.14770.4001-0.1060.0446-0.1044-0.05510.10710.1586-0.02290.01940.12480.00040.090929.308-7.63117.493
70.8978-0.27370.20512.4235-0.62041.84120.13920.1475-0.0699-0.2209-0.15330.16110.0297-0.28340.01410.06850.0597-0.04310.1266-0.03960.07211.1872.576-2.015
81.0030.0986-0.09991.88780.36751.4361-0.0232-0.0895-0.13190.3922-0.1164-0.03440.2471-0.13690.13970.1489-0.0131-0.02760.0814-0.0090.07238.488-7.70517.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A257 - 362
2X-RAY DIFFRACTION2A363 - 476
3X-RAY DIFFRACTION3B260 - 362
4X-RAY DIFFRACTION4B363 - 480
5X-RAY DIFFRACTION5A27 - 150
6X-RAY DIFFRACTION6A151 - 250
7X-RAY DIFFRACTION7B28 - 150
8X-RAY DIFFRACTION8B151 - 250

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