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- PDB-3gw9: Crystal structure of sterol 14-alpha demethylase (CYP51) from Try... -

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Entry
Database: PDB / ID: 3gw9
TitleCrystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei bound to an inhibitor N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxaziazol-2-yl)benzamide
ComponentsSTEROL 14ALPHA-DEMETHYLASE
KeywordsOXIDOREDUCTASE / STEROL 14ALPHA-DEMETHYLASE / CYP51 / CYTOCHROME P450 / HEME / MONOOXYGENASE / STEROL BIOSYNTHESIS / LIPIDS / ENDOPLASMIC RETICULUM / IRON / HEME-THIOLATE PROTEIN
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-VNI / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLepesheva, G.I. / Hargrove, T.Y. / Harp, J. / Wawrzak, Z. / Waterman, M.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections.
Authors: Lepesheva, G.I. / Park, H.W. / Hargrove, T.Y. / Vanhollebeke, B. / Wawrzak, Z. / Harp, J.M. / Sundaramoorthy, M. / Nes, W.D. / Pays, E. / Chaudhuri, M. / Villalta, F. / Waterman, M.R.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)208,55612
Polymers204,0734
Non-polymers4,4838
Water12,448691
1
A: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1393
Polymers51,0181
Non-polymers1,1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1393
Polymers51,0181
Non-polymers1,1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1393
Polymers51,0181
Non-polymers1,1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: STEROL 14ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1393
Polymers51,0181
Non-polymers1,1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.078, 79.113, 115.998
Angle α, β, γ (deg.)74.74, 79.13, 68.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
STEROL 14ALPHA-DEMETHYLASE


Mass: 51018.258 Da / Num. of mol.: 4 / Mutation: R28K, P29G, T30K, D31L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cellular location: membraneBiological membrane / Gene: CYP51, Tb11.02.4080 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / 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-VNI / N-[(1R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl]-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide / VNI (molecule)


Mass: 504.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H19Cl2N5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, POTASSIUM PHOSPHATE, n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE, N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxaziazol-2-yl)benzamide , pH 7.3, VAPOR ...Details: PEG 3350, POTASSIUM PHOSPHATE, n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE, N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxaziazol-2-yl)benzamide , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.87→37.48 Å / Num. all: 149012 / Num. obs: 144527 / % possible obs: 96.99 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 3.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.8 / % possible all: 91.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G1Q

3g1q


Resolution: 1.87→37.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.426 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 1.8 / σ(I): 1.8 / ESU R: 0.534 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 7635 5 %RANDOM
Rwork0.18861 ---
obs0.19111 144527 96.99 %-
all-149012 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.06 Å20 Å2
2---0.23 Å20.11 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.87→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14273 0 312 691 15276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210445
X-RAY DIFFRACTIONr_angle_refined_deg1.5492.02120286
X-RAY DIFFRACTIONr_angle_other_deg0.943325371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04351793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97923.241651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.427152616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.98215120
X-RAY DIFFRACTIONr_chiral_restr0.090.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023005
X-RAY DIFFRACTIONr_mcbond_it1.3551.59005
X-RAY DIFFRACTIONr_mcbond_other0.6281.53566
X-RAY DIFFRACTIONr_mcangle_it2.12214609
X-RAY DIFFRACTIONr_scbond_it2.98735951
X-RAY DIFFRACTIONr_scangle_it4.4984.55677
X-RAY DIFFRACTIONr_rigid_bond_restr1.51325401
X-RAY DIFFRACTIONr_sphericity_free10.3783691
X-RAY DIFFRACTIONr_sphericity_bonded3.816325029
LS refinement shellResolution: 1.87→1.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 484 -
Rwork0.279 9685 -
obs--88.01 %

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