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- PDB-4lxj: Saccharomyces cerevisiae lanosterol 14-alpha demethylase with lan... -

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Basic information

Entry
Database: PDB / ID: 4lxj
TitleSaccharomyces cerevisiae lanosterol 14-alpha demethylase with lanosterol bound
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / Cytochrome p450
Function / homology
Function and homology information


Endogenous sterols / Cholesterol biosynthesis / ergosterol biosynthetic process / sterol 14-demethylase activity / sterol 14alpha-demethylase / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / 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 / LANOSTEROL / OXYGEN MOLECULE / Lanosterol 14-alpha demethylase CYP51
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMonk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D.A. / O'Connell III, J.D. / Cannon, R.D. / McDonald, J. / Rodriguez, A. / Finer-Moore, J. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Structure summary
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5464
Polymers61,4711
Non-polymers1,0753
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.213, 67.005, 80.378
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 61470.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERG11, CYP51, YHR007C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10614, 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-LAN / LANOSTEROL


Mass: 426.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50O
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: 49% PEG 400, 100mM Glycine pH 9.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 64791 / Num. obs: 62523 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.2 % / Rsym value: 0.531 / % possible all: 72.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LD6

3ld6


Resolution: 1.9→29.327 Å / SU ML: 0.2 / σ(F): 1.38 / Phase error: 26.16 / Stereochemistry target values: ML
Details: VISUAL INSPECTION OF THE ELECTRON DENSITY MAPS AND A HIGH REAL SPACE R-FACTOR INDICATED THE NEED FOR CONSIDERABLE CARE IN PLACEMENT OF THE LIGAND IN THE LANOSTEROL CO-STRUCTURE. MINIMALLY ...Details: VISUAL INSPECTION OF THE ELECTRON DENSITY MAPS AND A HIGH REAL SPACE R-FACTOR INDICATED THE NEED FOR CONSIDERABLE CARE IN PLACEMENT OF THE LIGAND IN THE LANOSTEROL CO-STRUCTURE. MINIMALLY BIASED FO-FC ELECTRON DENSITY OMIT MAPS, CALCULATED WITH LANOSTEROL OMITTED TO CORRECTLY PLACE THE LANOSTEROL, RESULTED IN A REASONABLE CORRELATION COEFFICIENT (0.813).
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3117 4.99 %Random
Rwork0.195 ---
obs0.1966 62492 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 76 182 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114492
X-RAY DIFFRACTIONf_angle_d1.4236108
X-RAY DIFFRACTIONf_dihedral_angle_d15.0581666
X-RAY DIFFRACTIONf_chiral_restr0.086649
X-RAY DIFFRACTIONf_plane_restr0.006769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92970.37711030.31761998X-RAY DIFFRACTION73
1.9297-1.96130.34161080.31192235X-RAY DIFFRACTION79
1.9613-1.99510.34191140.29832456X-RAY DIFFRACTION89
1.9951-2.03140.27291370.27222693X-RAY DIFFRACTION96
2.0314-2.07050.31211360.25682752X-RAY DIFFRACTION98
2.0705-2.11270.27111580.24282760X-RAY DIFFRACTION99
2.1127-2.15870.23731460.23012748X-RAY DIFFRACTION99
2.1587-2.20880.24741600.20932720X-RAY DIFFRACTION99
2.2088-2.26410.23671490.2092761X-RAY DIFFRACTION99
2.2641-2.32530.23641550.20312760X-RAY DIFFRACTION99
2.3253-2.39370.25271180.19542789X-RAY DIFFRACTION99
2.3937-2.47090.22591510.18832753X-RAY DIFFRACTION99
2.4709-2.55910.20561420.1882791X-RAY DIFFRACTION99
2.5591-2.66150.23761380.18442762X-RAY DIFFRACTION100
2.6615-2.78260.2391370.1912815X-RAY DIFFRACTION100
2.7826-2.92920.22971450.18962767X-RAY DIFFRACTION99
2.9292-3.11250.23591610.18972764X-RAY DIFFRACTION99
3.1125-3.35250.2171500.20052800X-RAY DIFFRACTION100
3.3525-3.68930.22431400.18112814X-RAY DIFFRACTION100
3.6893-4.22180.2241710.17642787X-RAY DIFFRACTION100
4.2218-5.31380.19141490.17092813X-RAY DIFFRACTION100
5.3138-29.33010.2161490.2012837X-RAY DIFFRACTION98

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