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- PDB-2x2n: X-ray structure of cyp51 from trypanosoma brucei in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2x2n
TitleX-ray structure of cyp51 from trypanosoma brucei in complex with posaconazole in two different conformations
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE
KeywordsOXIDOREDUCTASE / P450 / METAL-BINDING / METHYLTRANSFERASE / 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 / POSACONAZOLE / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJan 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: LANOSTEROL 14-ALPHA-DEMETHYLASE
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
C: LANOSTEROL 14-ALPHA-DEMETHYLASE
D: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,47512
Polymers215,2064
Non-polymers5,2698
Water4,504250
1
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
D: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2386
Polymers107,6032
Non-polymers2,6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-60.2 kcal/mol
Surface area35960 Å2
MethodPISA
2
A: LANOSTEROL 14-ALPHA-DEMETHYLASE
C: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2386
Polymers107,6032
Non-polymers2,6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-61.2 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.892, 114.527, 138.087
Angle α, β, γ (deg.)90.00, 131.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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: 4 / Auth seq-ID: 30 - 475 / Label seq-ID: 16 - 461

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.5787, 0.007597, 0.8155), (0.003225, -0.9999, 0.0116), (0.8156, 0.009344, 0.5786)43.32, -12.8, -22.47
2given(0.7935, 0.1353, 0.5933), (0.1035, -0.9908, 0.08756), (0.5997, -0.008094, -0.8002)-21.41, -20.77, 57.37
3given(-0.03055, -0.1183, -0.9925), (-0.0381, 0.9924, -0.1171), (0.9988, 0.03424, -0.03482)103, 9.1, -2.66

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Components

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


Mass: 53801.492 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-481 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FIRST 21 RESIDUES UPSTREAM OF K22 WERE REPLACED WITH THE FRAGMENT MAKKKKK, 8XHIS TAG AT THE C-TERMINUS AND THREE MUTATIONS IN THE CODING SEQUENCE E249A/E250A/E251A WERE ENGINEERED
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-X2N / POSACONAZOLE / Posaconazole


Mass: 700.777 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H42F2N8O4 / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 249 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 250 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 249 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 250 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 251 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 249 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 250 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 251 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 249 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 250 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 251 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 249 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 250 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 251 TO ALA

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 8 / Details: 6% PEG 4000, 2% TACSIMATE, PH 8.0, 2% DMSO

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.6→21.25 Å / Num. obs: 71168 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 62.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

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

2wv2


Resolution: 2.6→102.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 28.089 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3572 5 %RANDOM
Rwork0.191 ---
obs0.195 67580 99.7 %-
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: 45.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.67 Å2
2---0.76 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→102.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13990 0 376 250 14616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210213
X-RAY DIFFRACTIONr_angle_refined_deg1.7492.02220146
X-RAY DIFFRACTIONr_angle_other_deg0.981324797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5451784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33723.039635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.612152475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.30315120
X-RAY DIFFRACTIONr_chiral_restr0.0870.22191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022996
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_it0.5841.58956
X-RAY DIFFRACTIONr_mcbond_other0.1931.53540
X-RAY DIFFRACTIONr_mcangle_it1.062214502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5435852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5924.55644
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.841325021
X-RAY DIFFRACTIONr_sphericity_free6.7353253
X-RAY DIFFRACTIONr_sphericity_bonded0.945324637
Refine LS restraints NCS

Ens-ID: 1 / Number: 5729 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.50.5
2Bmedium positional0.430.5
3Cmedium positional0.450.5
4Dmedium positional0.460.5
1Amedium thermal0.382
2Bmedium thermal0.352
3Cmedium thermal0.382
4Dmedium thermal0.542
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 314 -
Rwork0.314 4934 -
obs--99.79 %
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)
11.2432-0.1061-0.25080.8296-0.06690.8037-0.01350.1641-0.1681-0.09770.04220.06910.0417-0.1111-0.02880.0133-0.0109-0.00830.0336-0.01680.044626.573-24.66622.156
21.18640.02620.10940.35680.01910.68960.03880.09670.3084-0.0570.03050.0639-0.08110.1255-0.06930.0207-0.01620.01260.06130.03430.118246.19112.25911.863
30.77280.113-0.05460.60870.11290.95110.040.01280.0971-0.05050.0781-0.0702-0.0639-0.0083-0.11810.0154-0.00380.03710.0107-0.00150.101716.52110.86356.222
4000000000000000000000000
51.9653-3.9422-2.85168.57094.4936.5197-0.6771-0.0232-0.09171.2335-0.2093-0.11721.01290.68060.88630.589-0.2535-0.08290.53780.36810.65231.969-23.21531.812
610.3065-9.47032.77729.5971-2.5280.7494-0.1280.223-0.0540.57520.07730.0308-0.03540.06150.05070.26990.0079-0.00280.1498-0.00650.228251.1959.93220.644
72.91394.8397-2.913810.08461.134721.37550.2146-0.204-0.22020.2213-0.3479-0.42870.19470.50670.13330.6370.25050.08350.13120.07690.183525.3069.26351.887
812.396-2.9093-1.51466.11514.92274.1007-0.0690.416-1.1024-1.0229-0.17630.5526-0.8946-0.03530.24530.297-0.0965-0.13160.14690.00820.460837.365-22.65972.96
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 477
2X-RAY DIFFRACTION2B30 - 477
3X-RAY DIFFRACTION3C30 - 477
4X-RAY DIFFRACTION4D30 - 477
5X-RAY DIFFRACTION5A1480
6X-RAY DIFFRACTION6B1479
7X-RAY DIFFRACTION7C1479
8X-RAY DIFFRACTION8D1479

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