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- PDB-4uym: Crystal structure of sterol 14-alpha demethylase (CYP51B) from a ... -

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Basic information

Entry
Database: PDB / ID: 4uym
TitleCrystal structure of sterol 14-alpha demethylase (CYP51B) from a pathogenic filamentous fungus Aspergillus fumigatus in complex with voriconazole
Components14-ALPHA STEROL DEMETHYLASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / HEME / MONOOXYGENASE / STEROL BIOSYNTHESIS / EUKARYOTIC MEMBRANES / CYTOCHROME P450 FOLD / ENDOPLASMIC RETICULUM MEMBRANE
Function / homology
Function and homology information


ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / oxidoreductase activity / iron ion binding ...ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / methyltransferase activity / monooxygenase activity / methylation / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / 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 / Voriconazole / Sterol 14-alpha demethylase cyp51B / 14-alpha sterol demethylase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure-Functional Characterization of Cytochrome P450 Sterol Alpha-Demethylase (Cyp51B) from Aspergillus Fumigatus and Molecular Basis for the Development of Antifungal Drugs
Authors: Hargrove, T.Y. / Warwzak, Z. / Lamb, D.C. / Guengerich, F.P. / Lepesheva, G.I.
History
DepositionSep 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,4316
Polymers106,5002
Non-polymers1,9324
Water2,936163
1
A: 14-ALPHA STEROL DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2163
Polymers53,2501
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 14-ALPHA STEROL DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2163
Polymers53,2501
Non-polymers9662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.193, 109.193, 90.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein 14-ALPHA STEROL DEMETHYLASE / STEROL 14-ALPHA DEMETHYLASE / CYP51B


Mass: 53249.812 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 50-519 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Gene: ERG 11 / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174
References: UniProt: Q96W81, UniProt: E9QY26*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-VOR / Voriconazole / (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 349.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14F3N5O / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.88 Å3/Da / Density % sol: 57.2 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2014 / Details: BE LENSES DIAMOND LAUE
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 36885 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UYL

4uyl


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 11.224 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 1939 5 %RANDOM
Rwork0.20959 ---
obs0.21108 36885 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.586 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 136 163 7803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0197861
X-RAY DIFFRACTIONr_bond_other_d0.0050.027387
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.98210699
X-RAY DIFFRACTIONr_angle_other_deg0.697317018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2065938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84123.237346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.084151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8431550
X-RAY DIFFRACTIONr_chiral_restr0.0740.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218794
X-RAY DIFFRACTIONr_gen_planes_other0.010.021856
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_it7.2247.6193758
X-RAY DIFFRACTIONr_mcbond_other7.2237.6183757
X-RAY DIFFRACTIONr_mcangle_it10.03311.4324694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.4218.0894103
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.553→2.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 136 -
Rwork0.298 2596 -
obs--94.4 %

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