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- PDB-8xdv: O-methyltransferase from Lycoris longituba M52S-F186Y variant com... -

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Basic information

Entry
Database: PDB / ID: 8xdv
TitleO-methyltransferase from Lycoris longituba M52S-F186Y variant complexed with Mg and SAH
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
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
S-ADENOSYL-L-HOMOCYSTEINE / norbelladine O-methyltransferase
Similarity search - Component
Biological speciesLycoris longituba (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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)55,6486
Polymers54,8302
Non-polymers8174
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-45 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.951, 80.894, 116.107
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: 27415.229 Da / Num. of mol.: 2 / Mutation: M52S/F186Y
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 23% (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: 2.32→47.16 Å / Num. obs: 39195 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.6
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2027 / CC1/2: 0.891 / % 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: 2.32→47.16 Å / SU ML: 0.3148 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.1037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 1914 4.88 %
Rwork0.2155 37281 -
obs0.2167 39195 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.62 Å2
Refinement stepCycle: LAST / Resolution: 2.32→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 0 94 3953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214104
X-RAY DIFFRACTIONf_angle_d0.55285607
X-RAY DIFFRACTIONf_chiral_restr0.0432627
X-RAY DIFFRACTIONf_plane_restr0.0034730
X-RAY DIFFRACTIONf_dihedral_angle_d18.9534595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.33191450.32882680X-RAY DIFFRACTION99.61
2.38-2.440.36571350.30552624X-RAY DIFFRACTION99.64
2.44-2.510.33961470.30772686X-RAY DIFFRACTION99.93
2.51-2.60.30351120.28062665X-RAY DIFFRACTION99.36
2.6-2.690.30271470.26322652X-RAY DIFFRACTION99.57
2.69-2.80.31771670.27362659X-RAY DIFFRACTION99.82
2.8-2.920.30661160.26312668X-RAY DIFFRACTION99.71
2.92-3.080.29811350.26412608X-RAY DIFFRACTION97.65
3.08-3.270.23661540.23252666X-RAY DIFFRACTION99.82
3.27-3.520.22421170.2172669X-RAY DIFFRACTION99.93
3.52-3.880.20471390.20192681X-RAY DIFFRACTION100
3.88-4.440.20431590.16912640X-RAY DIFFRACTION99.93
4.44-5.590.19591150.17212716X-RAY DIFFRACTION100
5.59-47.160.19891260.17462667X-RAY DIFFRACTION99.75

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