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- PDB-1gsz: Crystal Structure of a Squalene Cyclase in Complex with the Poten... -

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Basic information

Entry
Database: PDB / ID: 1gsz
TitleCrystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic Drug Ro48-8071
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / CHOLESTEROL BIOSYNTHESIS / INHIBITOR OXIDOSQUALENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN
Function / homology
Function and homology information


squalene-hopanol cyclase / squalene-hopene cyclase / squalene-hopene cyclase activity / lanosterol synthase activity / triterpenoid biosynthetic process / ergosterol biosynthetic process / cholesterol 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 and squalene oxidase repeat / 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 and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Chem-R71 / Squalene--hopene cyclase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å
AuthorsLenhart, A. / Weihofen, W.A. / Pleschke, A.E.W. / Schulz, G.E.
Citation
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.
#1: 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.
#2: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#3: Journal: Protein Sci. / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Squalene-Hopene Cyclase from Alicyclobacillus Acidocaldarius
Authors: Wendt, K.U. / Feil, C. / Lenhart, A. / 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
DepositionJan 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4May 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)217,2159
Polymers214,9503
Non-polymers2,2646
Water4,594255
1
A: SQUALENE--HOPENE CYCLASE
hetero molecules

B: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8106
Polymers143,3002
Non-polymers1,5104
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)144,8106
Polymers143,3002
Non-polymers1,5104
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)144,8106
Polymers143,3002
Non-polymers1,5104
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)140.897, 140.897, 244.049
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(-0.484541, -0.874759, -0.004148), (0.874768, -0.484542, -0.000834), (-0.001281, -0.004033, 0.999991)141.123, -5.245, 1.529
2given(-0.529047, 0.848507, -0.012053), (-0.848531, -0.529126, -0.004461), (-0.010162, 0.007867, 0.999917)77.886, 121.444, 0.369
3given(-0.485848, -0.873918, -0.014797), (0.874022, -0.485884, -0.001242), (-0.006104, -0.013536, 0.99989)141.88901, -4.447, -0.369

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Components

#1: Protein SQUALENE--HOPENE CYCLASE


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-R71 / [4-({6-[ALLYL(METHYL)AMINO]HEXYL}OXY)-2-FLUOROPHENYL](4-BROMOPHENYL)METHANONE / Ro 48-8071


Mass: 448.368 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27BrFNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE CREATION OF HOPENE BY CYCLIZATION OF SQUALENE.
Sequence detailsMET 1 IS NOT IN SWISS-PROT ENTRY. RESIDUES UP TO ALA 10 AND AFTER ILE 628 HAVE NO ELECTRON DENSITY ...MET 1 IS NOT IN SWISS-PROT ENTRY. RESIDUES UP TO ALA 10 AND AFTER ILE 628 HAVE NO ELECTRON DENSITY (ALL PDB-NUMBERING).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP WITH 5...8 MG/ML PROTEIN, 0.3 % (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO ...Details: HANGING DROP WITH 5...8 MG/ML PROTEIN, 0.3 % (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO PROTEIN) RO48-8071 IN THE STARTING DROPLET. RESERVOIR CONTAINED 100 MM SODIUM CITRATE (PH 4.8), 100 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15-8 mg/mlSHC1drop
20.3 %(w/v)C8E41reservoir
350 mM1reservoirNaCl
450 mMsodium citrate1reservoirpH4.8
53-8 %(v/v)satPEG6001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: SIEMENS MULTIWIRE / 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→30 Å / Num. obs: 54249 / % possible obs: 78.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.4 / % possible all: 47.6
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 79 % / Num. measured all: 156593 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 48 %

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1989 2.9 %RANDOM
Rwork0.203 ---
obs0.203 54200 78 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0971 Å2 / ksol: 0.259545 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å24.68 Å20 Å2
2---2.15 Å20 Å2
3---4.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14892 0 147 255 15294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
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
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 206 3.8 %
Rwork0.384 5234 -
obs--47.7 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 3.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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