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- PDB-2sqc: SQUALENE-HOPENE CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS -

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Basic information

Entry
Database: PDB / ID: 2sqc
TitleSQUALENE-HOPENE CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS
ComponentsSQUALENE-HOPENE CYCLASE
KeywordsISOMERASE / TRITERPENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN / QW-SEQUENCE / 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 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
Squalene--hopene cyclase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionAug 2, 1998Processing site: BNL
Revision 1.0Apr 27, 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0838
Polymers143,2442
Non-polymers1,8396
Water27,2931515
1
A: SQUALENE-HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2353
Polymers71,6221
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SQUALENE-HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8485
Polymers71,6221
Non-polymers1,2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.820, 118.820, 276.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, -0.007, 0.054), (0.008, -1, 0.018), (0.054, 0.019, 0.998)
Vector: 114.844, 117.469, -4.2373)

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Components

#1: Protein SQUALENE-HOPENE CYCLASE /


Mass: 71622.031 Da / Num. of mol.: 2 / Mutation: D376C, C435S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Cell line: JM105 / Cellular location: MEMBRANEBiological 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-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMODEL OF THE PROPOSED CATALYTIC BASE IS INDICATED BY ATOM O HOH 1 98.147 29.292 33.208 1.00 28.41

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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: 3.4 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.3 %(w/v)detergent1drop
350 mMsodium citrate1drop
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 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→49 Å / Num. obs: 523124 / % possible obs: 90.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.062 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.146 / % possible all: 59
Reflection
*PLUS
Num. obs: 120483 / Num. measured all: 523124 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 59 % / Num. unique obs: 5694 / Num. measured obs: 9054 / Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQC

1sqc


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18
Details: INITIAL REFINEMENT USING XPLOR, FOLLOWED BY REFINEMENT USING REFMAC. THE BULK SOLVENT CORRECTION OF X-PLOR USED THROUGHOUT THE REFINEMENT. PRODUCT HOPENE MODELED IN ACTIVE SITE (SEE THE ...Details: INITIAL REFINEMENT USING XPLOR, FOLLOWED BY REFINEMENT USING REFMAC. THE BULK SOLVENT CORRECTION OF X-PLOR USED THROUGHOUT THE REFINEMENT. PRODUCT HOPENE MODELED IN ACTIVE SITE (SEE THE LITERATURE FOR HOPENE NOMENCLATURE) C1 HOP X 13 103.614 31.179 20.850 1.00 20.00 C2 HOP X 13 104.002 31.723 19.469 1.00 20.00 C3 HOP X 13 102.849 32.537 18.869 1.00 20.00 C4 HOP X 13 102.333 33.739 19.747 1.00 20.00 C5 HOP X 13 102.047 33.170 21.166 1.00 20.00 C6 HOP X 13 101.550 34.176 22.155 1.00 20.00 C7 HOP X 13 100.764 33.510 23.240 1.00 20.00 C8 HOP X 13 101.590 32.510 24.080 1.00 20.00 C9 HOP X 13 102.405 31.574 23.074 1.00 20.00 C10 HOP X 13 103.110 32.276 21.878 1.00 20.00 C11 HOP X 13 103.240 30.601 23.915 1.00 20.00 C12 HOP X 13 102.398 29.750 24.828 1.00 20.00 C13 HOP X 13 101.537 30.606 25.808 1.00 20.00 C14 HOP X 13 100.665 31.555 24.953 1.00 20.00 C15 HOP X 13 99.813 32.389 26.001 1.00 20.00 C22 HOP X 13 99.698 30.849 30.226 1.00 20.00 C23 HOP X 13 103.398 34.803 19.717 1.00 20.00 C24 HOP X 13 101.099 34.259 19.068 1.00 20.00 C25 HOP X 13 104.383 33.039 22.288 1.00 20.00 C26 HOP X 13 102.570 33.339 24.968 1.00 20.00 C27 HOP X 13 99.678 30.771 24.088 1.00 20.00 C28 HOP X 13 100.156 28.456 26.313 1.00 20.00 C29 HOP X 13 98.842 29.609 30.376 1.00 20.00 C30 HOP X 13 99.828 31.851 31.405 1.00 20.00
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6059 5.3 %RANDOM
Rwork0.153 ---
obs-114164 90 %-
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9988 0 126 1515 11629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor Rfree: 0.239 / Num. reflection Rwork: 4807 / Rfactor obs: 0.196

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