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- PDB-9no6: Structure of csTOS the Terpinolene Synthase from Cannabis sativa -

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Basic information

Entry
Database: PDB / ID: 9no6
TitleStructure of csTOS the Terpinolene Synthase from Cannabis sativa
ComponentsTerpinolene synthase
KeywordsBIOSYNTHETIC PROTEIN / terpinolene synthase / Cannabis sativa / plant protein
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 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
Terpinolene synthase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWiles, D. / Roest, J. / Vivivan, J.P. / Beddoe, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Struct.Biol. / Year: 2025
Title: The product specificities of terpinolene synthase, from cannabis sativa, reveals the plasticity of the terpene synthase active site.
Authors: Wiles, D. / Roest, J. / Vivan, J.P. / Beddoe, T.
History
DepositionMar 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terpinolene synthase


Theoretical massNumber of molelcules
Total (without water)74,8791
Polymers74,8791
Non-polymers00
Water1,910106
1
A: Terpinolene synthase

A: Terpinolene synthase


Theoretical massNumber of molelcules
Total (without water)149,7582
Polymers149,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2560 Å2
ΔGint-12 kcal/mol
Surface area43310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 118.413, 204.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-667-

HOH

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Components

#1: Protein Terpinolene synthase


Mass: 74879.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A5C1IZK1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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

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 EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→80 Å / Num. obs: 17259 / % possible obs: 87.8 % / Redundancy: 5.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.562 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 863 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→80 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 709 4.98 %
Rwork0.2173 --
obs0.2199 14234 69.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 0 106 4251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.493
X-RAY DIFFRACTIONf_dihedral_angle_d15.2541571
X-RAY DIFFRACTIONf_chiral_restr0.034610
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.3042500.2344981X-RAY DIFFRACTION26
2.69-2.960.27971040.27691894X-RAY DIFFRACTION50
2.96-3.390.29971360.25682875X-RAY DIFFRACTION75
3.39-4.280.28071880.20623842X-RAY DIFFRACTION99
4.28-800.24882310.19773933X-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)
10.01550.0155-0.0030.0655-0.00340.0260.11850.12410.03810.00520.10760.149-0.08950.09810.00760.3588-0.0607-0.01930.2779-0.04350.261335.01385.335974.7401
20.03980.03130.02070.03630.04010.08080.1924-0.1120.00720.26330.0016-0.00560.070.07440.0090.3786-0.1296-0.01080.33530.02510.215932.270274.630699.373
30.1124-0.0070.02820.1001-0.08640.0742-0.1115-0.11020.07870.06060.01050.1961-0.1552-0.0004-0.00510.2625-0.03580.00970.2174-0.00960.192123.95383.484478.0726
40.06740.0195-0.10040.02880.03930.37310.0803-0.03690.018-0.047-0.0063-0.0308-0.10920.10270.04550.1232-0.0058-0.00730.12270.03020.274619.660966.589965.9129
50.0054-0.02240.00460.0645-0.01190.15040.0360.093-0.01710.03380.070.14950.14370.01720.2552-0.1477-0.09270.09680.12130.11420.208221.168951.146865.6102
60.0764-0.02980.0340.03590.03160.10410.0496-0.053-0.01420.1027-0.01510.0762-0.005-0.1593-0.07370.3186-0.0280.12050.10820.07950.087615.579958.656587.1691
70.05650.00410.06870.20290.15740.21950.0863-0.009-0.04440.10740.039-0.1304-0.00820.15770.03310.1367-0.02590.04640.2553-0.05250.300427.018771.139377.2138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 299 )
5X-RAY DIFFRACTION5chain 'A' and (resid 300 through 445 )
6X-RAY DIFFRACTION6chain 'A' and (resid 446 through 506 )
7X-RAY DIFFRACTION7chain 'A' and (resid 507 through 562 )

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