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- PDB-3sqc: SQUALENE-HOPENE CYCLASE -

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Basic information

Entry
Database: PDB / ID: 3sqc
TitleSQUALENE-HOPENE CYCLASE
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / TRITERPENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN / QW-SEQUENCE REPEAT / CHOLESTEROL BIOSYNTHESIS
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWendt, K.U. / Schulz, G.E.
Citation
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.
#1: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#2: 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 4, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)214,9143
Polymers214,9143
Non-polymers00
Water2,054114
1
A: SQUALENE--HOPENE CYCLASE


Theoretical massNumber of molelcules
Total (without water)71,6381
Polymers71,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SQUALENE--HOPENE CYCLASE


Theoretical massNumber of molelcules
Total (without water)71,6381
Polymers71,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SQUALENE--HOPENE CYCLASE


Theoretical massNumber of molelcules
Total (without water)71,6381
Polymers71,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.960, 140.960, 243.800
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(-0.48133, -0.87654, 0.00092), (0.87653, -0.48134, -0.00238), (0.00253, -0.00034, 1)140.73573, -5.49561, 1.18225
2given(-0.53212, 0.84657, -0.01287), (-0.84664, -0.53217, -0.00036), (-0.00715, 0.01071, 0.99992)78.35586, 121.19873, 0.08305
3given(-0.48593, -0.87388, -0.01451), (0.87398, -0.48595, -0.00232), (-0.00503, -0.0138, 0.99989)141.95891, -4.4695, -0.46764

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Components

#1: Protein SQUALENE--HOPENE CYCLASE


Mass: 71638.094 Da / Num. of mol.: 3 / Mutation: D376C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Wendt, K.U., (1997) Protein Sci., 6, 722.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
20.6 %(w/v)C8E41drop
30.1 Msodium citrate1reservoir
41dropH2O

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 57421 / % possible obs: 83 % / Redundancy: 3.9 % / Rsym value: 0.047 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.17 / % possible all: 44

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQC

1sqc


Resolution: 2.8→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2890 5 %RANDOM
Rwork0.209 ---
obs0.209 57229 82.4 %-
Displacement parametersBiso mean: 50 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å / Luzzati d res low obs: 4.6 Å / Luzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14886 0 0 114 15000
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_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.93 Å
RfactorNum. reflection% reflection
Rfree0.36 206 5.5 %
Rwork0.36 3688 -
obs--45 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04

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