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- PDB-10ee: Cannabis sativa O methyl transferase 1 -

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Basic information

Entry
Database: PDB / ID: 10ee
TitleCannabis sativa O methyl transferase 1
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: 1.65 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)44,0887
Polymers43,3421
Non-polymers7466
Water4,954275
1
A: O-methyltransferase 1
hetero molecules

A: O-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,17614
Polymers86,6852
Non-polymers1,49112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area10700 Å2
ΔGint-83 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.990, 89.990, 217.210
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
Components on special symmetry positions
IDModelComponents
11A-405-

ACT

21A-405-

ACT

31A-761-

HOH

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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) / Gene: G4B88_018487 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / 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.: 275 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM ammonium acetate, 100 mM BIS-Tris pH 5.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→44.06 Å / Num. obs: 63341 / % possible obs: 99.97 % / Redundancy: 39.4 % / Biso Wilson estimate: 25.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1306 / Net I/σ(I): 21.78
Reflection shellResolution: 1.65→1.709 Å / Rmerge(I) obs: 2.65 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6194 / CC1/2: 0.732 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.06 Å / SU ML: 0.1447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.9275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1732 3167 5 %
Rwork0.1548 60166 -
obs0.1557 63333 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.69 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 24 275 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892881
X-RAY DIFFRACTIONf_angle_d0.95823896
X-RAY DIFFRACTIONf_chiral_restr0.0564432
X-RAY DIFFRACTIONf_plane_restr0.0068496
X-RAY DIFFRACTIONf_dihedral_angle_d14.31711069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.28561350.26122569X-RAY DIFFRACTION100
1.67-1.70.2461350.22622566X-RAY DIFFRACTION100
1.7-1.730.2381350.20872572X-RAY DIFFRACTION100
1.73-1.760.19411350.20132559X-RAY DIFFRACTION100
1.76-1.790.21581350.1962571X-RAY DIFFRACTION100
1.79-1.820.24021350.20552560X-RAY DIFFRACTION100
1.82-1.860.19141350.19092575X-RAY DIFFRACTION100
1.86-1.90.18861360.16652572X-RAY DIFFRACTION100
1.9-1.950.1911360.16272580X-RAY DIFFRACTION100
1.95-20.16911360.14932586X-RAY DIFFRACTION100
2-2.050.17061360.14322594X-RAY DIFFRACTION100
2.05-2.110.16311360.13272576X-RAY DIFFRACTION100
2.11-2.180.15211370.13242599X-RAY DIFFRACTION99.96
2.18-2.260.15911360.13832598X-RAY DIFFRACTION100
2.26-2.350.16071370.14042593X-RAY DIFFRACTION100
2.35-2.450.16931380.13272625X-RAY DIFFRACTION99.96
2.45-2.580.13941380.13272614X-RAY DIFFRACTION100
2.58-2.740.14261380.13722621X-RAY DIFFRACTION100
2.74-2.960.17271380.14482637X-RAY DIFFRACTION100
2.96-3.250.18121410.14092676X-RAY DIFFRACTION100
3.25-3.720.13471420.14312685X-RAY DIFFRACTION99.96
3.72-4.690.16241430.13812727X-RAY DIFFRACTION100
4.69-44.990.21441540.20052911X-RAY DIFFRACTION99.67
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)
11.002159831250.8227107604271.202315036932.116564906742.042039254783.65142569713-0.002404801524240.130791055452-0.0413662626716-0.0183594412378-0.0276649837236-0.11895755776-0.03476193159880.0468855830924-0.0147319033660.1739644857660.01711030789340.03946193343820.2120160155420.04742509148180.1894116282410.91261011920450.262621628-30.7881059374
23.67121660368-0.421296357956-2.644292807462.253915721510.3627005987364.4818665787-0.1000958208590.511214992733-0.225226608367-0.26624510263-0.0417462805961-0.1119362595290.37854218082-0.2368206014090.1474795890850.2070338938340.002278551700050.007109171911280.242800348798-0.009695414345290.16454114194-0.93874265492540.6385365256-34.4032365693
31.034542714140.6121981254840.05918709291931.472217433980.01686283988610.782174437843-0.05075500464960.0304730357727-0.108770055911-0.03991347720360.07295354221880.04132510882460.103218863389-0.0920316580311-0.00962025413420.222510070268-0.005297754978090.03901554158530.2498035341430.04117316122110.231721647796-18.18464334835.2875832921-11.9305991978
42.066103824940.37363615035-0.3970009220582.18380618815-0.6629554148351.650660785090.0476675721486-0.197461646658-0.2807965221910.15616916739-0.0643240970152-0.1498422925950.07468994158940.1195387079190.009893232017530.239488282088-0.0003046229963570.00581352166230.2761757976610.06132408415050.264677139764-9.0232264497632.2320980178-1.59802287327
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 6 through 77 )6 - 771 - 72
22chain 'A' and (resid 78 through 128 )78 - 12873 - 123
33chain 'A' and (resid 129 through 258 )129 - 258124 - 253
44chain 'A' and (resid 259 through 368 )259 - 368254 - 354

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