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- PDB-1w6j: Structure of human OSC in complex with Ro 48-8071 -

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Basic information

Entry
Database: PDB / ID: 1w6j
TitleStructure of human OSC in complex with Ro 48-8071
ComponentsLANOSTEROL SYNTHASE
KeywordsISOMERASE / CYCLASE / CHOLESTEROL / LANOSTEROL / MONOTOPIC MEMBRANE PROTEIN / B-OCTYL-GLUCOSIDE / STEROID BIOSYNTHESIS
Function / homology
Function and homology information


lanosterol synthase / lanosterol synthase activity / triterpenoid biosynthetic process / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / lipid droplet / Activation of gene expression by SREBF (SREBP) / regulation of protein stability / endoplasmic reticulum membrane / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase and squalene oxidase repeat ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Special / Mainly Alpha
Similarity search - Domain/homology
TETRADECANE / Chem-R71 / Lanosterol synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThoma, R. / Schulz-Gasch, T. / D'Arcy, B. / Benz, J. / Aebi, J. / Dehmlow, H. / Hennig, M. / Ruf, A.
Citation
Journal: Nature / Year: 2004
Title: Insight Into Steroid Scaffold Formation from the Structure of Human Oxidosqualene Cyclase
Authors: Thoma, R. / Schulz-Gasch, T. / D'Arcy, B. / Benz, J. / Aebi, J. / Dehmlow, H. / Hennig, M. / Stihle, M. / Ruf, A.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: The Monotopic Membrane Protein Human Osc is Active as Monomer
Authors: Ruf, A. / Muller, F. / D'Arcy, B. / Stihle, M. / Kuznir, E. / Handschin, C. / Morand, O. / Thoma, R.
History
DepositionAug 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LANOSTEROL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9316
Polymers83,4071
Non-polymers1,5245
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)189.915, 202.424, 62.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LANOSTEROL SYNTHASE / / OXIDOSQUALENE--LANOSTEROL CYCLASE / OXIDO SQUALENE CYCLASE / 2 / 3-EPOXYSQUALENE--LANOSTEROL CYCLASE / OSC


Mass: 83406.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P48449, lanosterol synthase
#2: Chemical ChemComp-R71 / [4-({6-[ALLYL(METHYL)AMINO]HEXYL}OXY)-2-FLUOROPHENYL](4-BROMOPHENYL)METHANONE / Ro 48-8071


Mass: 448.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27BrFNO2
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE CYCLIZATION OF (S)-2,3 OXIDOSQUALENE TO LANOSTEROL, A REACTION THAT FORMS THE STEROL ...CATALYZES THE CYCLIZATION OF (S)-2,3 OXIDOSQUALENE TO LANOSTEROL, A REACTION THAT FORMS THE STEROL NUCLEUS. BELONGS TO THE TERPENE CYCLASE/MUTASE FAMILY.
Nonpolymer details(C14) UNIDENTIFIED LIPID FRAGMENT, MODELLED AS LINEAR CARBON CHAIN

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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: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growDetails: 25% (W/V) PEG3350 0.4M AMMONIUM ACETATE 0.1M TRIS PH 8.5 10% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92004
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92004 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 60002 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2SQC

2sqc


Resolution: 2.2→141.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.02 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3033 5.1 %RANDOM
Rwork0.17 ---
obs0.171 56956 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---2.79 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 90 416 6330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216081
X-RAY DIFFRACTIONr_bond_other_d0.0010.025402
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9378246
X-RAY DIFFRACTIONr_angle_other_deg0.831312520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63222.905296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3451550
X-RAY DIFFRACTIONr_chiral_restr0.0710.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
X-RAY DIFFRACTIONr_nbd_refined0.2050.21304
X-RAY DIFFRACTIONr_nbd_other0.1840.25412
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.53704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01525779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3932776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2194.52467
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 194
Rwork0.23 3984

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