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- PDB-8xe3: norbelladine 4'-O-methyltransferase complexed with Mg and SAH -

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Basic information

Entry
Database: PDB / ID: 8xe3
Titlenorbelladine 4'-O-methyltransferase complexed with Mg and SAH
ComponentsNorbelladine 4'-O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase family protein / NpN4OMT
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
S-ADENOSYL-L-HOMOCYSTEINE / Norbelladine 4'-O-methyltransferase
Similarity search - Component
Biological speciesNarcissus pseudonarcissus MK-2014 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 4'-O-methyltransferase
B: Norbelladine 4'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8889
Polymers54,7942
Non-polymers1,0947
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-44 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.548, 80.096, 115.771
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 4'-O-methyltransferase


Mass: 27397.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Narcissus pseudonarcissus MK-2014 (plant)
Gene: N4OMT / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A077EWA5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / 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.: 401 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (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: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 1.72→46.92 Å / Num. obs: 92520 / % possible obs: 98.1 % / Redundancy: 8.4 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.4
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2441 / CC1/2: 0.735 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→46.92 Å / SU ML: 0.1653 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.8558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 4560 4.93 %
Rwork0.1597 87960 -
obs0.1616 92520 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.72 Å2
Refinement stepCycle: LAST / Resolution: 1.72→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 18 401 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914094
X-RAY DIFFRACTIONf_angle_d1.0375586
X-RAY DIFFRACTIONf_chiral_restr0.0619625
X-RAY DIFFRACTIONf_plane_restr0.0061718
X-RAY DIFFRACTIONf_dihedral_angle_d18.5824597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.32011200.2632821X-RAY DIFFRACTION92.05
1.74-1.760.28621560.25562867X-RAY DIFFRACTION96.37
1.76-1.780.26081320.23812901X-RAY DIFFRACTION96.01
1.78-1.80.24091510.21692865X-RAY DIFFRACTION96.73
1.8-1.830.26571460.21772931X-RAY DIFFRACTION96.46
1.83-1.850.24981640.20392863X-RAY DIFFRACTION96.9
1.85-1.880.21651770.20032890X-RAY DIFFRACTION97.33
1.88-1.910.24351530.19222929X-RAY DIFFRACTION96.92
1.91-1.940.22751720.19732877X-RAY DIFFRACTION97.91
1.94-1.970.21771620.1742943X-RAY DIFFRACTION97.52
1.97-20.18451640.17552905X-RAY DIFFRACTION97
2-2.040.2091590.1652883X-RAY DIFFRACTION97.91
2.04-2.080.21291360.17532983X-RAY DIFFRACTION98.08
2.08-2.120.19331470.16042914X-RAY DIFFRACTION97.83
2.12-2.170.211330.15722993X-RAY DIFFRACTION97.75
2.17-2.220.15881780.15782851X-RAY DIFFRACTION97.99
2.22-2.270.17081520.15632975X-RAY DIFFRACTION98.4
2.27-2.330.20171370.15632968X-RAY DIFFRACTION98.54
2.33-2.40.1741520.16422971X-RAY DIFFRACTION98.55
2.4-2.480.22481150.16333009X-RAY DIFFRACTION98.58
2.48-2.570.22891590.15622932X-RAY DIFFRACTION98.31
2.57-2.670.18751520.1572917X-RAY DIFFRACTION98.43
2.67-2.790.19471290.16152994X-RAY DIFFRACTION98.95
2.79-2.940.22151740.16342953X-RAY DIFFRACTION98.71
2.94-3.130.21781670.17062922X-RAY DIFFRACTION97.97
3.13-3.370.21681520.15452953X-RAY DIFFRACTION99.04
3.37-3.70.17981590.14052985X-RAY DIFFRACTION99.59
3.71-4.240.18351350.12743007X-RAY DIFFRACTION99.52
4.24-5.340.16191480.13072993X-RAY DIFFRACTION99.71
5.34-46.920.17721790.15872965X-RAY DIFFRACTION99.46

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