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- PDB-8xe0: O-methyltransferase from Lycoris longituba M52W variant complexed... -

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Basic information

Entry
Database: PDB / ID: 8xe0
TitleO-methyltransferase from Lycoris longituba M52W variant complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde
Componentsnorbelladine O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase family protein / LlOMT
Function / homology
Function and homology information


norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE / norbelladine O-methyltransferase
Similarity search - Component
Biological speciesLycoris longituba (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaw, Y.Y.H. / Nakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H02777 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15303 Japan
CitationJournal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.
History
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: norbelladine O-methyltransferase
B: norbelladine O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9527
Polymers54,9972
Non-polymers9565
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-35 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.421, 80.862, 116.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein norbelladine O-methyltransferase


Mass: 27498.361 Da / Num. of mol.: 2 / Mutation: M52W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycoris longituba (plant) / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A6B9TNK2
#2: Chemical ChemComp-H6N / Protocatechuic aldehyde


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 14% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.048 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.048 Å / Relative weight: 1
ReflectionResolution: 2.2→47.29 Å / Num. obs: 46653 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 42.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.156 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2124 / CC1/2: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.29 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.7035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 2339 5.01 %
Rwork0.2028 44314 -
obs0.2044 46653 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 10 81 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024051
X-RAY DIFFRACTIONf_angle_d0.55545531
X-RAY DIFFRACTIONf_chiral_restr0.0425622
X-RAY DIFFRACTIONf_plane_restr0.0032709
X-RAY DIFFRACTIONf_dihedral_angle_d16.3101572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.35161360.31762572X-RAY DIFFRACTION99.74
2.25-2.290.38471280.29732632X-RAY DIFFRACTION99.78
2.29-2.350.31141350.29172592X-RAY DIFFRACTION99.63
2.35-2.410.34491260.29982628X-RAY DIFFRACTION99.57
2.41-2.470.33231440.25282594X-RAY DIFFRACTION99.93
2.47-2.540.24011290.26322620X-RAY DIFFRACTION99.78
2.54-2.630.25041420.22752624X-RAY DIFFRACTION99.78
2.63-2.720.28071450.22032581X-RAY DIFFRACTION99.63
2.72-2.830.32121240.23062612X-RAY DIFFRACTION99.78
2.83-2.960.24081360.22812651X-RAY DIFFRACTION99.86
2.96-3.110.21111350.21322574X-RAY DIFFRACTION99.82
3.11-3.310.23741760.20872558X-RAY DIFFRACTION99.85
3.31-3.560.29371230.19552628X-RAY DIFFRACTION99.96
3.56-3.920.23991440.18892621X-RAY DIFFRACTION100
3.92-4.490.1821410.16192604X-RAY DIFFRACTION100
4.49-5.650.20081540.17052600X-RAY DIFFRACTION100
5.66-47.290.17691210.18112623X-RAY DIFFRACTION99.6

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