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- PDB-9waz: O-methyltransferase PoOMT1/SAH -

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Basic information

Entry
Database: PDB / ID: 9waz
TitleO-methyltransferase PoOMT1/SAH
ComponentsO-methyltransferase PoOMT1
KeywordsTRANSFERASE / PoOMT/SAH
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesPaeonia ostii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsWei, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Functional and structural characterization of an O-methyltransferase involved in the paralled biosynthesis of paeonol in tree peony
Authors: Wei, H.
History
DepositionAug 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-methyltransferase PoOMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6832
Polymers40,2991
Non-polymers3841
Water3,531196
1
A: O-methyltransferase PoOMT1
hetero molecules

A: O-methyltransferase PoOMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3664
Polymers80,5972
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9390 Å2
ΔGint-58 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.381, 123.385, 87.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein O-methyltransferase PoOMT1


Mass: 40298.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paeonia ostii (plant) / Production host: Escherichia coli (E. coli)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M Hepes (pH 7.5), and 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.03→61.69 Å / Num. obs: 23093 / % possible obs: 99.2 % / Redundancy: 12.5 % / Biso Wilson estimate: 24.86 Å2 / CC1/2: 0.963 / Net I/σ(I): 6.1
Reflection shellResolution: 2.03→2.08 Å / Num. unique obs: 1681 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→57.77 Å / SU ML: 0.1828 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2221 1133 4.91 %
Rwork0.1838 21931 -
obs0.1857 23064 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.32 Å2
Refinement stepCycle: LAST / Resolution: 2.03→57.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 26 196 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372860
X-RAY DIFFRACTIONf_angle_d0.72653880
X-RAY DIFFRACTIONf_chiral_restr0.046443
X-RAY DIFFRACTIONf_plane_restr0.0059489
X-RAY DIFFRACTIONf_dihedral_angle_d6.6288377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.120.25441410.20142709X-RAY DIFFRACTION99.41
2.12-2.230.24731430.19172723X-RAY DIFFRACTION99.79
2.23-2.370.2281420.19172707X-RAY DIFFRACTION99.75
2.37-2.560.25041370.20032736X-RAY DIFFRACTION99.97
2.56-2.810.24831480.19772758X-RAY DIFFRACTION99.97
2.82-3.220.23591500.19472745X-RAY DIFFRACTION99.93
3.22-4.060.18851490.16972635X-RAY DIFFRACTION95.31
4.06-57.770.20511230.17062918X-RAY DIFFRACTION99.48
Refinement TLS params.Method: refined / Origin x: 4.21790996937 Å / Origin y: 18.4221236865 Å / Origin z: -6.06305139854 Å
111213212223313233
T0.169685506651 Å2-0.0105946266783 Å20.00277174911254 Å2-0.164079628049 Å20.011469589227 Å2--0.16507938535 Å2
L0.289151337071 °2-0.0206212446721 °20.141967930781 °2-0.357533831011 °20.0837523127748 °2--0.426451777073 °2
S-0.00405710906956 Å °-0.0401685646183 Å °-0.00277002422547 Å °0.0885636645453 Å °-0.0254253466091 Å °-0.0323492715612 Å °0.0153045120443 Å °-0.0467022812608 Å °-3.4257285121E-6 Å °
Refinement TLS groupSelection details: all

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