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- PDB-1sqc: SQUALENE-HOPENE-CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS -

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Basic information

Entry
Database: PDB / ID: 1sqc
TitleSQUALENE-HOPENE-CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS
ComponentsSQUALENE-HOPENE CYCLASE
KeywordsISOMERASE / MEMBRANE PROTEIN / TERPENOID METABOLISM / SQUALENE TO HOPENE (HOP-22 / 29-ENE) AND DIPLOPTEROL (HOPANE-22-OL)
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
Squalene--hopene cyclase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.85 Å
AuthorsWendt, K.U. / Schulz, G.E.
Citation
Journal: Science / Year: 1997
Title: Structure and function of a squalene cyclase.
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#1: 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.
History
DepositionSep 1, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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.process_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8792
Polymers71,6501
Non-polymers2291
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.700, 140.700, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein SQUALENE-HOPENE CYCLASE


Mass: 71650.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Cell line: JM105 / Cellular location: MEMBRANE / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Cell line (production host): JM105 / Cellular location (production host): CYTOPLASMIC MEMBRANE / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P33247, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP CONTAINING: 8 MG/ML PROTEIN, 0.3% N-OCTYLTETRAOXYETHYLENE IN 50 MM SODIUM CITRATE, PH 4.8 WITH A RESERVOIR SOLUTION CONTAINING 100 MM SODIUM CITRATE, PH 4.8., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.3 %(w/v)C8E4(n-octyl-tetraoxyethylene)1drop
350 mMsodium citrate1drop
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 18914 / % possible obs: 86 % / Redundancy: 2.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.056 / Net I/σ(I): 11.9
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.36 / % possible all: 49
Reflection
*PLUS
Num. measured all: 53288 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 49 % / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
CCP4(AGROVATA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.85→20 Å / Rfactor Rfree error: 0.0077 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED-ATOMS (2 GROUPS P RESIDUE) / Cross valid method: THROUGHOUT / σ(F): 0
Details: STANDARD BULK SOLVENT CORRECTION OF X-PLOR 3.851 USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 989 5.2 %RANDOM
Rwork0.167 ---
obs0.167 18914 85.7 %-
Displacement parametersBiso mean: 43 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 16 38 5017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15

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