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- PDB-9wba: O-methyltransferase PoOMT1/SAH/4'-hydroxyacetophenone -

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Basic information

Entry
Database: PDB / ID: 9wba
TitleO-methyltransferase PoOMT1/SAH/4'-hydroxyacetophenone
ComponentsO-methyltransferase PoOMT1
KeywordsTRANSFERASE / O-methyltransferase PoOMT1/SAH/4'-hydroxyacetophenone
Function / homologyP-HYDROXYACETOPHENONE / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesPaeonia ostii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 1.0Aug 26, 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)40,8193
Polymers40,2991
Non-polymers5212
Water3,945219
1
A: O-methyltransferase PoOMT1
hetero molecules

A: O-methyltransferase PoOMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6396
Polymers80,5972
Non-polymers1,0414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10160 Å2
ΔGint-46 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.780, 122.810, 89.440
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-AC6 / P-HYDROXYACETOPHENONE


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris (pH 6.5), 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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.83→50.62 Å / Num. obs: 31729 / % possible obs: 98.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.1
Reflection shellResolution: 1.83→1.88 Å / Num. unique obs: 2015 / CC1/2: 0.578

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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: 1.83→32.4 Å / SU ML: 0.2133 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 1547 4.88 %
Rwork0.1977 30154 -
obs0.1989 31701 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.83→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 36 219 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312870
X-RAY DIFFRACTIONf_angle_d0.61163893
X-RAY DIFFRACTIONf_chiral_restr0.0427443
X-RAY DIFFRACTIONf_plane_restr0.006491
X-RAY DIFFRACTIONf_dihedral_angle_d6.518379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.890.37741110.30462365X-RAY DIFFRACTION86.12
1.89-1.960.29711210.25452607X-RAY DIFFRACTION94.13
1.96-2.030.24731260.23222746X-RAY DIFFRACTION99.48
2.03-2.130.28951430.21732769X-RAY DIFFRACTION99.97
2.13-2.240.23941540.20892765X-RAY DIFFRACTION100
2.24-2.380.25141500.21212749X-RAY DIFFRACTION100
2.38-2.560.23791150.20972829X-RAY DIFFRACTION100
2.56-2.820.2391440.20832783X-RAY DIFFRACTION100
2.82-3.230.22321980.19872754X-RAY DIFFRACTION100
3.23-4.070.19911210.17662858X-RAY DIFFRACTION100
4.07-32.40.17891640.17412929X-RAY DIFFRACTION99.84

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