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- PDB-1o79: Structures of human oxidosqualene cyclase inhibitors bound to an ... -

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Basic information

Entry
Database: PDB / ID: 1o79
TitleStructures of human oxidosqualene cyclase inhibitors bound to an homologous enzyme
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / CHOLESTEROL BIOSYNTHESIS / INHIBITOR / MONOTOPIC MEMBRANE PROTEIN
Function / homology
Function and homology information


squalene-hopanol cyclase / squalene-hopene cyclase / squalene-hopene cyclase activity / triterpenoid biosynthetic process / lipid droplet / lyase activity / plasma membrane
Similarity search - Function
Squalene hopene cyclase / 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 alpha-alpha toroid domain / Glycosyltransferase - #20 ...Squalene hopene cyclase / 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 alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Chem-R23 / Squalene--hopene cyclase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å
AuthorsLenhart, A. / Reinert, D.J. / Weihofen, W.A. / Aebi, J.D. / Dehmlow, H. / Morand, O.H. / Schulz, G.E.
Citation
Journal: J.Med.Chem. / Year: 2003
Title: Binding Structures and Potencies of Oxidosqualene Cyclase Inhibitors with the Homologous Squalene-Hopene Cyclase
Authors: Lenhart, A. / Reinert, D.J. / Aebi, J.D. / Dehmlow, H. / Morand, O.H. / Schulz, G.E.
#1: Journal: Chem.Biol. / Year: 2002
Title: Crystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic Drug Ro48-8071
Authors: Lenhart, A. / Weihofen, W.A. / Pleschke, A.E.W. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of the Membrane Protein Squalene-Hopene Cyclase at 2.0 A Resolution
Authors: Wendt, K.U. / Lenhart, A. / Schulz, G.E.
#3: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#4: Journal: J.Lipid Res. / Year: 1997
Title: Ro48-8071, a New 2,3-Oxidosqualene:Lanosterol Cyclase Inhibitor Lowering Plasma Cholesterol in Hamsters, Squirrel Monkeys, and Minipigs: Comparison to Simvastatin
Authors: Morand, O.H. / Aebi, J.D. / Dehmlow, H. / Ji, Y.H. / Gains, N. / Lengsfeld, H. / Himber, J.
History
DepositionOct 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: SQUALENE--HOPENE CYCLASE
B: SQUALENE--HOPENE CYCLASE
C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,1929
Polymers214,9503
Non-polymers2,2426
Water4,270237
1
A: SQUALENE--HOPENE CYCLASE
hetero molecules

B: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7956
Polymers143,3002
Non-polymers1,4954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
MethodPQS
2
B: SQUALENE--HOPENE CYCLASE
hetero molecules

A: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7956
Polymers143,3002
Non-polymers1,4954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+2/31
MethodPQS
3
C: SQUALENE--HOPENE CYCLASE
hetero molecules

C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7956
Polymers143,3002
Non-polymers1,4954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)141.289, 141.289, 245.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.47992, -0.87731, -0.00073), (0.87731, -0.47992, -0.00343), (0.00265, -0.00229, 0.99999)141.22539, -5.67247, 1.06708
2given(-0.53392, 0.84545, -0.01206), (-0.8455, -0.53398, -0.00208), (-0.0082, 0.00908, 0.99993)78.75256, 121.70016, 0.14779

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Components

#1: Protein SQUALENE--HOPENE CYCLASE / SHC


Mass: 71650.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): JM105 / References: UniProt: P33247, squalene-hopene cyclase
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-R23 / METHYL-[4-(4-PIPERIDINE-1-YLMETHYL-PHENYL)-CYCLOHEXYL]-CARBAMINIC ACID-(4-CHLOROPHENYL)-ESTER


Mass: 441.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H33ClN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES CYCLIZATION OF SQUALENE TO HOPENE. KEY ENZYME IN HOPANOID (TRITERPENOID) METABOLISM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 4.8 / Details: pH 4.80

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→43.03 Å / Num. obs: 54923 / % possible obs: 79.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 4.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.8→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 --RANDOM
Rwork0.2394 ---
obs0.2394 52186 74.2 %-
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14892 0 156 237 15285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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