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- PDB-9wb6: O-methyltransferase PoOMT1/SAH/2',4'-dihydroxyacetophenone -

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Basic information

Entry
Database: PDB / ID: 9wb6
TitleO-methyltransferase PoOMT1/SAH/2',4'-dihydroxyacetophenone
ComponentsO-methyltransferase PoOMT1
KeywordsTRANSFERASE / O-methyltransferase PoOMT1/SAH/2' / 4'-dihydroxyacetophenone
Function / homology: / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesPaeonia ostii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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)40,8353
Polymers40,2991
Non-polymers5372
Water91951
1
A: O-methyltransferase PoOMT1
hetero molecules

A: O-methyltransferase PoOMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6716
Polymers80,5972
Non-polymers1,0734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9270 Å2
ΔGint-56 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.550, 123.830, 87.630
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-A1EVU / 1-[2,4-bis(oxidanyl)phenyl]ethanone


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 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: 0.9793 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.28→50.57 Å / Num. obs: 16634 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 45.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 2.28→2.34 Å / Num. unique obs: 1227 / CC1/2: 0.791

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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: 2.28→34.95 Å / SU ML: 0.3103 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 861 5.18 %
Rwork0.2119 15754 -
obs0.2138 16615 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.45 Å2
Refinement stepCycle: LAST / Resolution: 2.28→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 37 51 2816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472830
X-RAY DIFFRACTIONf_angle_d0.71493837
X-RAY DIFFRACTIONf_chiral_restr0.0479436
X-RAY DIFFRACTIONf_plane_restr0.0056483
X-RAY DIFFRACTIONf_dihedral_angle_d6.4012373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.420.36661400.26522592X-RAY DIFFRACTION99.93
2.42-2.610.31941240.26582602X-RAY DIFFRACTION99.93
2.61-2.870.33121260.26062604X-RAY DIFFRACTION99.85
2.87-3.290.32091680.25522589X-RAY DIFFRACTION99.89
3.29-4.140.24161560.20382632X-RAY DIFFRACTION99.89
4.14-34.950.17461470.17352735X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 3.96829120249 Å / Origin y: 18.3685515554 Å / Origin z: -6.35713029193 Å
111213212223313233
T0.350950190942 Å2-0.0281683249192 Å20.00504779282734 Å2-0.332474496312 Å20.00363301716161 Å2--0.333648543555 Å2
L0.399117424047 °2-0.0303935556319 °20.384837860756 °2-0.444111326185 °2-0.0166630083956 °2--0.693647728082 °2
S0.00500289289148 Å °-0.105254925209 Å °0.0310824606063 Å °0.182121522353 Å °-0.0724131603214 Å °-0.0753191588734 Å °0.0353532702253 Å °-0.0654234762394 Å °-0.153949146548 Å °
Refinement TLS groupSelection details: all

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