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- PDB-1x8v: Estriol-bound and ligand-free structures of sterol 14alpha-demeth... -

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Basic information

Entry
Database: PDB / ID: 1x8v
TitleEstriol-bound and ligand-free structures of sterol 14alpha-demethylase (CYP51)
ComponentsCytochrome P450 51
KeywordsOXIDOREDUCTASE / alpha-beta / heme co-factor / protein-estriol complex
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
ESTRIOL / 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: 1.55 Å
AuthorsPodust, L.M. / Yermalitskaya, L.V. / Lepesheva, G.I. / Podust, V.N. / Dalmasso, E.A. / Waterman, M.R.
CitationJournal: Structure / Year: 2004
Title: Estriol Bound and Ligand-free Structures of Sterol 14alpha-Demethylase.
Authors: Podust, L.M. / Yermalitskaya, L.V. / Lepesheva, G.I. / Podust, V.N. / Dalmasso, E.A. / Waterman, M.R.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6714
Polymers51,4771
Non-polymers1,1933
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.161, 84.522, 110.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer

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Components

#1: Protein Cytochrome P450 51 / CYPLI / P450-LIA1 / Sterol 14-alpha demethylase / Lanosterol 14-alpha demethylase / P450-14DM


Mass: 51477.285 Da / Num. of mol.: 1 / Mutation: C37L, C442A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp51 / 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ESL / ESTRIOL / 1,3,5(10)-ESTRATRIENE-3,16,17-TRIOL


Mass: 288.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.12 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2004
Details: sagittal focusing crystal and vertically focusing mirror
RadiationMonochromator: Si (220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 65201 / Num. obs: 63041 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.073 / Net I/σ(I): 31.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 5483 / Rsym value: 0.37 / % possible all: 85.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E9X

1e9x


Resolution: 1.55→27.5 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 869366.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6064 10.1 %RANDOM
Rwork0.206 ---
all0.208 65201 --
obs0.206 60253 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.6078 Å2 / ksol: 0.423389 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.27 Å20 Å20 Å2
2---2.21 Å20 Å2
3----6.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.55→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 85 319 3821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.712
X-RAY DIFFRACTIONc_scangle_it4.362.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 849 10.2 %
Rwork0.275 7504 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3HEM.PARHEM.TOP

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