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- PDB-26ay: Crystal structure of SchOMT2-SAM-GOM from Schisandra chinensis -

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Basic information

Entry
Database: PDB / ID: 26ay
TitleCrystal structure of SchOMT2-SAM-GOM from Schisandra chinensis
ComponentsSchOMT2
KeywordsTRANSFERASE / O-methyltransferase / methyltransferase / SAM / GOM
Function / homology: / S-ADENOSYLMETHIONINE
Function and homology information
Biological speciesSchisandra chinensis (Chinese magnolia-vine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsYang, G.H. / Yang, J.Z. / Xiong, R.L. / Xu, R.
Funding support China, United Kingdom, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U23A20511 China
National Natural Science Foundation of China (NSFC)82574540 China
CAMS Innovation Fund for Medical Sciences (CIFMS)2025-I2M-XHXX-114 United Kingdom
CitationJournal: To Be Published
Title: Enzymatic and structural basis of lignan methylation diversity in Schisandra chinensis accelerates the discovery of anticancer drug resistance reversers
Authors: Xiong, R.L. / Xu, R. / Peng, S. / Yang, J.Z. / Xu, X. / Sun, D. / Gao, R.R. / Sun, Z.H. / Luo, Y. / Yan, M.Z. / Yang, G.H. / Li, B. / Liu, J.S. / Xu, Z.C. / Liu, H.T.
History
DepositionApr 24, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SchOMT2
B: SchOMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8115
Polymers83,6262
Non-polymers1,1853
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-67 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.740, 95.740, 181.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

21B-524-

HOH

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Components

#1: Protein SchOMT2


Mass: 41812.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schisandra chinensis (Chinese magnolia-vine)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1E80 / (9~{S},10~{R})-3,4,15,16-tetramethoxy-9,10-dimethyl-tricyclo[10.4.0.0^{2,7}]hexadeca-1(12),2(7),3,5,13,15-hexaene-5,14-diol / Gomisin J


Mass: 388.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M (Ca(CH3COO)2.H2O 0.1M Sodium cacodylate pH6.5 38%PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.21→95.87 Å / Num. obs: 42246 / % possible obs: 97.2 % / Redundancy: 19.6 % / Biso Wilson estimate: 61.69 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.078 / Net I/σ(I): 7.4
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6211 / CC1/2: 0.448 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→18.78 Å / SU ML: 0.4336 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2636 1635 5.03 %
Rwork0.2122 30875 -
obs0.2149 32510 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.05 Å2
Refinement stepCycle: LAST / Resolution: 2.43→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 82 59 5527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835588
X-RAY DIFFRACTIONf_angle_d0.99337556
X-RAY DIFFRACTIONf_chiral_restr0.0572838
X-RAY DIFFRACTIONf_plane_restr0.0084958
X-RAY DIFFRACTIONf_dihedral_angle_d11.2527742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.50.43751380.38662537X-RAY DIFFRACTION99.96
2.5-2.580.381080.33272518X-RAY DIFFRACTION99.58
2.58-2.670.36191340.2932548X-RAY DIFFRACTION99.93
2.67-2.780.35451290.26332518X-RAY DIFFRACTION99.89
2.78-2.910.34021250.25792551X-RAY DIFFRACTION99.89
2.91-3.060.35341520.24262530X-RAY DIFFRACTION100
3.06-3.250.30851380.2392533X-RAY DIFFRACTION99.85
3.25-3.50.30531380.22672556X-RAY DIFFRACTION99.96
3.5-3.850.27321300.20992601X-RAY DIFFRACTION99.89
3.85-4.40.22431520.18352571X-RAY DIFFRACTION99.78
4.4-5.520.2211350.18282645X-RAY DIFFRACTION100
5.52-18.780.2221560.18442767X-RAY DIFFRACTION99.69

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