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- PDB-10ef: Cannabis sativa O-methyl transferase 1 - DHR soak -

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Basic information

Entry
Database: PDB / ID: 10ef
TitleCannabis sativa O-methyl transferase 1 - DHR soak
ComponentsO-methyltransferase 1
KeywordsTRANSFERASE / O-methyltransferase / dihydroresveratrol
Function / homologyACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsForrester, T.J.B. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2020-07113 Canada
CitationJournal: J.Nat.Prod. / Year: 2026
Title: Cell-Free Synthesis of Cannabistilbene I: A Dual Acting Anti-Inflammatory from Cannabis sativa .
Authors: Boddington, K.F. / Soubeyrand, E. / Van Gelder, K. / Perrin, C. / Forrester, T.J.B. / Holborn, J. / Casaretto, J.A. / Al-Abdul-Wahid, M.S. / Piotrowski, M.L. / Magolan, J. / Lalonde, J. / ...Authors: Boddington, K.F. / Soubeyrand, E. / Van Gelder, K. / Perrin, C. / Forrester, T.J.B. / Holborn, J. / Casaretto, J.A. / Al-Abdul-Wahid, M.S. / Piotrowski, M.L. / Magolan, J. / Lalonde, J. / Kimber, M.S. / Rothstein, S.J. / Akhtar, T.A.
History
DepositionJan 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers43,3421
Non-polymers5954
Water1,72996
1
A: O-methyltransferase 1
hetero molecules

A: O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,87410
Polymers86,6852
Non-polymers1,1898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area9710 Å2
ΔGint-88 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.500, 90.500, 217.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein O-methyltransferase 1


Mass: 43342.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium citrate dibasic, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.181 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.25→44.3 Å / Num. obs: 25903 / % possible obs: 99.95 % / Redundancy: 19 % / Biso Wilson estimate: 51.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08473 / Net I/σ(I): 28.71
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 19.4 % / Rmerge(I) obs: 2.571 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2517 / CC1/2: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.3 Å / SU ML: 0.3064 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1999 7.72 %
Rwork0.1829 23897 -
obs0.1859 25896 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 14 96 2870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082845
X-RAY DIFFRACTIONf_angle_d0.8893848
X-RAY DIFFRACTIONf_chiral_restr0.0517428
X-RAY DIFFRACTIONf_plane_restr0.0071487
X-RAY DIFFRACTIONf_dihedral_angle_d14.55271039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.40151390.3431659X-RAY DIFFRACTION100
2.31-2.370.27281380.25211658X-RAY DIFFRACTION99.83
2.37-2.440.3121400.25321674X-RAY DIFFRACTION100
2.44-2.520.35551390.27061670X-RAY DIFFRACTION100
2.52-2.610.28321400.23381668X-RAY DIFFRACTION100
2.61-2.710.21121400.18441674X-RAY DIFFRACTION100
2.71-2.830.24761420.1851687X-RAY DIFFRACTION99.89
2.83-2.980.25381400.20091678X-RAY DIFFRACTION100
2.98-3.170.27391410.19941690X-RAY DIFFRACTION100
3.17-3.420.23841440.17521712X-RAY DIFFRACTION100
3.42-3.760.21811430.17131721X-RAY DIFFRACTION100
3.76-4.30.19131460.15521730X-RAY DIFFRACTION100
4.3-5.420.20491470.15341766X-RAY DIFFRACTION99.95
5.42-44.30.16751600.18021910X-RAY DIFFRACTION99.9
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)
10.4207685768880.8724040718160.7517220036354.871232902213.20308764394.12247043404-0.03676739564350.202797692256-0.122841527972-0.08583204936750.0775839122827-0.239951554744-0.04844103987590.0440766319522-0.06024929144170.2993324052190.01501470448530.02549300482340.4044478355090.03461824416780.3440050652441.1581080122150.4769178979-31.1445217178
23.12866728103-1.80813651835-2.860872997242.390647388333.581568320297.405093807910.1990934763650.453849314107-0.0534136750737-0.0730105324005-0.1240413419010.0221534672836-0.0280301769785-0.357290770381-0.07683007319780.300288631066-0.00344323055965-0.01769101688740.2982738395660.06229434336110.292837602774-2.8316083951345.120290501-27.7788037639
32.055881903230.8009852676620.1339074816711.64267350319-0.08213928812540.7757575775830.0558206195406-0.0522660687259-0.2754744149660.0974944863527-0.032041533985-0.152816892830.0658770388950.0218237356127-0.01326304539640.404992563846-0.006370234672440.02630448919790.3748685980180.01905397365220.372747417336-14.110426462532.0590475727-7.3196230957
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 77 )7 - 771 - 71
22chain 'A' and (resid 78 through 144 )78 - 14472 - 136
33chain 'A' and (resid 145 through 368 )145 - 368137 - 351

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