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- PDB-9ops: Structural Insights into Monoterpene Cyclisation of Limonene Synt... -

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Basic information

Entry
Database: PDB / ID: 9ops
TitleStructural Insights into Monoterpene Cyclisation of Limonene Synthase from Cannabis sativa
Components(-)-limonene synthase TPS1, chloroplastic
KeywordsLYASE / terpene synthase / metal ion binding / plastid
Function / homology
Function and homology information


terpinolene synthase / (+)-beta-pinene synthase / (4S)-limonene synthase / (4S)-limonene synthase activity / myrcene synthase / myrcene synthase activity / (R)-limonene synthase / (R)-limonene synthase activity / (+)-alpha-pinene synthase / pinene synthase activity ...terpinolene synthase / (+)-beta-pinene synthase / (4S)-limonene synthase / (4S)-limonene synthase activity / myrcene synthase / myrcene synthase activity / (R)-limonene synthase / (R)-limonene synthase activity / (+)-alpha-pinene synthase / pinene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
(-)-limonene synthase TPS1, chloroplastic
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWiles, D. / Roest, J. / Vivian, J.P. / Beddoe, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural insights into monoterpene cyclisation of limonene synthase from Cannabis sativa.
Authors: Wiles, D. / Roest, J. / Vivian, J.P. / Beddoe, T.
History
DepositionMay 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (-)-limonene synthase TPS1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)66,4081
Polymers66,4081
Non-polymers00
Water27015
1
A: (-)-limonene synthase TPS1, chloroplastic

A: (-)-limonene synthase TPS1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)132,8172
Polymers132,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2530 Å2
ΔGint-8 kcal/mol
Surface area42980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.336, 97.336, 117.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein (-)-limonene synthase TPS1, chloroplastic / (-)-(4S)-limonene synthase / (+)-alpha-pinene synthase TPS1 / (+)-beta-pinene synthase TPS1 / (R)- ...(-)-(4S)-limonene synthase / (+)-alpha-pinene synthase TPS1 / (+)-beta-pinene synthase TPS1 / (R)-limonene synthase / Myrcene synthase TPS1 / Terpene synthase 1 / CsTPS1 / Terpene synthase 14 CT / CsTPS14CT / Terpinolene synthase TPS1


Mass: 66408.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: TPS1, TPS14CT / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A7IZZ1, (4S)-limonene synthase, (+)-alpha-pinene synthase, (+)-beta-pinene synthase, (R)-limonene synthase, myrcene synthase, terpinolene synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM Tris-HCl (pH 7.0), 100 mM MgCl2, 100 mM NaCl, 30% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.2→60 Å / Num. obs: 10899 / % possible obs: 99.1 % / Redundancy: 7.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.29 / Net I/σ(I): 7.5
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.45 / Num. unique obs: 545 / CC1/2: 0.12 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.84 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 625 5.75 %
Rwork0.2296 --
obs0.2328 10877 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 0 15 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034392
X-RAY DIFFRACTIONf_angle_d0.5915923
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711629
X-RAY DIFFRACTIONf_chiral_restr0.041633
X-RAY DIFFRACTIONf_plane_restr0.003751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.29621560.27892536X-RAY DIFFRACTION100
3.52-4.030.30421780.24282491X-RAY DIFFRACTION98
4.03-5.050.26421350.21082595X-RAY DIFFRACTION100
5.06-19.840.28221560.20132630X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1379-0.1522-0.23351.1894-0.25240.6737-0.12650.0155-0.2103-0.3678-0.05460.19870.3543-0.1385-0.4930.2864-0.15860.03320.35380.23540.208614.9529-0.073939.5967
21.03220.44320.06721.1231-0.47020.78340.14940.123-0.037-0.0513-0.0731-0.3699-0.27790.36730.07580.3365-0.04160.01170.16450.05520.266434.702418.780331.1678
31.2695-0.25450.19330.6548-0.24150.69520.01930.1572-0.1274-0.2361-0.08730.1841-0.03430.09390.14210.2938-0.0577-0.06480.12630.03140.26034.660711.754731.5412
40.6120.1914-0.11810.4756-0.09750.71550.0256-0.09270.33860.192-0.07550.11530.0915-0.21650.11270.30240.0452-0.160.2219-0.09910.2492-3.393331.293231.0061
51.8156-0.1535-0.35561.5709-0.42130.9326-0.14410.23950.393-0.3422-0.2671-0.1198-0.39640.09840.03940.3965-0.0516-0.12320.21280.05290.233316.509530.071924.7942
61.25940.5763-0.66041.94510.83361.31310.09680.48760.3763-0.7301-0.23460.282-0.1788-0.29790.07820.4439-0.1161-0.07080.5039-0.04430.49813.3468.157421.6538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 432 )
5X-RAY DIFFRACTION5chain 'A' and (resid 433 through 522 )
6X-RAY DIFFRACTION6chain 'A' and (resid 523 through 550 )

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