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- PDB-2vku: 4,4'-Dihydroxybenzophenone Mimics Sterol Substrate in the Binding... -

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Basic information

Entry
Database: PDB / ID: 2vku
Title4,4'-Dihydroxybenzophenone Mimics Sterol Substrate in the Binding Site of Sterol 14alpha-Demethylase (CYP51) in the X-ray Structure of the Complex
ComponentsCYTOCHROME P450 51
KeywordsOXIDOREDUCTASE / STEROID BIOSYNTHESIS / CYP51-4 / CYTOPLASM / ALPHA-BETA / HEME CO-FACTOR / LIPID SYNTHESIS / STEROL BIOSYNTHESIS / 4'-DIHYDROXYBENZOPHENONE COMPLEX / NADP / IRON / HEME / MONOOXYGENASE / METAL-BINDING
Function / homology
Function and homology information


sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol biosynthetic process / sterol metabolic process / bile acid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity ...sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol biosynthetic process / sterol metabolic process / bile acid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / cholesterol homeostasis / oxidoreductase activity / iron ion binding / heme binding / cytoplasm / cytosol
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
bis(4-hydroxyphenyl)methanone / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase / Sterol 14alpha-demethylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEddine, A.N. / von Kries, J.P. / Podust, M.V. / Podust, L.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: X-Ray Structure of 4,4'-Dihydroxybenzophenone Mimicking Sterol Substrate in the Active Site of Sterol 14Alpha-Demethylase (Cyp51)
Authors: Eddine, A.N. / P Von Kries, J. / Podust, M.V. / Warrier, T. / Kaufmann, S.H.E. / Podust, L.M.
History
DepositionDec 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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_conn
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,52712
Polymers51,4771
Non-polymers2,05011
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.734, 82.095, 85.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 51 / CYPLI / P450-LIA1 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14-ALPHA DEMETHYLASE / P450-14DM / ...CYPLI / P450-LIA1 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14-ALPHA DEMETHYLASE / P450-14DM / STEROL 14ALPHA-DEMETHYLASE


Mass: 51477.285 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 4 HIS RESIDUES ARE ENGINEERED AT THE C-TERMINUS / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0A512, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase
#2: Chemical
ChemComp-DBE / bis(4-hydroxyphenyl)methanone


Mass: 214.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10O3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 37 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS 442 TO ALA
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): COORDINATED TO C394 VIA THIOLATE BOND
Sequence detailsMUTATIONS C37L AND C442A. 4 HIS RESIDUES WERE ENGINEERED 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growTemperature: 296 K / pH: 7.5
Details: 1.2 M LI SULFATE, 0.1 M HEPES, 7.5, 2% ISOPROPANOL, T=23 C

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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: Nov 29, 2007 / 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: 1.95→50 Å / Num. obs: 40591 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CIB

2cib


Resolution: 1.95→47.17 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 127450.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4009 9.9 %RANDOM
Rwork0.177 ---
obs0.177 40519 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6839 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.95 Å20 Å20 Å2
2---0.81 Å20 Å2
3----4.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 137 518 4177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 644 10 %
Rwork0.21 5827 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3DBP.PARDBP.TOP

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