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- PDB-6o9q: Wild-type SaSQS1 -

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Basic information

Entry
Database: PDB / ID: 6o9q
TitleWild-type SaSQS1
ComponentsSesquisabinene B synthase 1
KeywordsLYASE / Terpene / Cyclase / Sesquisabinene
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase ...Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Sesquisabinene B synthase 1
Similarity search - Component
Biological speciesSantalum album (white sandalwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlank, P.N. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)0000-0002-9842-210X United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structure of Sesquisabinene Synthase 1, a Terpenoid Cyclase That Generates a Strained [3.1.0] Bridged-Bicyclic Product.
Authors: Blank, P.N. / Shinsky, S.A. / Christianson, D.W.
History
DepositionMar 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sesquisabinene B synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6026
Polymers65,2951
Non-polymers3075
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, SDS PAGE and LCMSMS was used to confirm the identity of the protein of interest.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.420, 85.840, 220.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Sesquisabinene B synthase 1


Mass: 65294.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Santalum album (white sandalwood) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0RDR2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% (v/v) Tacsimate, 0.1 M MES monohydrate (pH = 6.0), 25% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→60.95 Å / Num. obs: 47868 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 11 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3065 / CC1/2: 0.58 / Rpim(I) all: 0.457 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UV0

5uv0


Resolution: 1.9→60.945 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.16
RfactorNum. reflection% reflection
Rfree0.2315 2382 4.98 %
Rwork0.1917 --
obs0.1937 47844 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→60.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 20 295 4440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074244
X-RAY DIFFRACTIONf_angle_d0.8575752
X-RAY DIFFRACTIONf_dihedral_angle_d4.6842493
X-RAY DIFFRACTIONf_chiral_restr0.048631
X-RAY DIFFRACTIONf_plane_restr0.007729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.36021600.33062634X-RAY DIFFRACTION100
1.9388-1.9810.35541280.30042656X-RAY DIFFRACTION100
1.981-2.02710.37361290.28022614X-RAY DIFFRACTION100
2.0271-2.07780.26331530.26152642X-RAY DIFFRACTION100
2.0778-2.13390.271490.24172631X-RAY DIFFRACTION100
2.1339-2.19670.27171170.21612662X-RAY DIFFRACTION100
2.1967-2.26760.25791550.20862660X-RAY DIFFRACTION100
2.2676-2.34870.26851380.20052629X-RAY DIFFRACTION100
2.3487-2.44270.23051310.20242677X-RAY DIFFRACTION100
2.4427-2.55390.22831390.19852648X-RAY DIFFRACTION100
2.5539-2.68860.23791390.19922649X-RAY DIFFRACTION100
2.6886-2.8570.2211370.20152687X-RAY DIFFRACTION100
2.857-3.07760.26491500.2032659X-RAY DIFFRACTION100
3.0776-3.38730.26051300.20132702X-RAY DIFFRACTION100
3.3873-3.87730.22371460.17312702X-RAY DIFFRACTION100
3.8773-4.88470.18221420.15172746X-RAY DIFFRACTION100
4.8847-60.97640.20131390.1792864X-RAY DIFFRACTION100

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