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- PDB-8xdr: O-methyltransferase from Lycoris aurea complexed with Mg, SAH, an... -

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Basic information

Entry
Database: PDB / ID: 8xdr
TitleO-methyltransferase from Lycoris aurea complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / O-methyltransferase family protein / LaOMT
Function / homologyProtocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesLycoris aurea (golden hurricane-lily)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,10810
Polymers54,8472
Non-polymers1,2628
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-33 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.373, 81.091, 116.770
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

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Protein , 1 types, 2 molecules AB

#1: Protein O-methyltransferase family protein


Mass: 27423.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycoris aurea (golden hurricane-lily) / Production host: Escherichia coli M15 (bacteria)

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Non-polymers , 6 types, 387 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-H6N / Protocatechuic aldehyde


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% (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: 1.83→47.38 Å / Num. obs: 78525 / % possible obs: 98.6 % / Redundancy: 8.3 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2469 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→47.38 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 21.0378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 3949 5.03 %
Rwork0.1665 74576 -
obs0.1684 78525 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.42 Å2
Refinement stepCycle: LAST / Resolution: 1.83→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 8 379 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01014076
X-RAY DIFFRACTIONf_angle_d1.03755553
X-RAY DIFFRACTIONf_chiral_restr0.0613622
X-RAY DIFFRACTIONf_plane_restr0.0061712
X-RAY DIFFRACTIONf_dihedral_angle_d16.9933589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.31911600.28622569X-RAY DIFFRACTION97.01
1.85-1.880.29161340.2762627X-RAY DIFFRACTION97.39
1.88-1.90.32321510.26792703X-RAY DIFFRACTION97.71
1.9-1.930.27531340.2482607X-RAY DIFFRACTION97.2
1.93-1.950.31851590.24052628X-RAY DIFFRACTION97.82
1.95-1.980.29521450.23382655X-RAY DIFFRACTION97.56
1.98-2.010.28271240.2212652X-RAY DIFFRACTION97.88
2.01-2.050.22981370.2012659X-RAY DIFFRACTION98.07
2.05-2.080.25891700.19372617X-RAY DIFFRACTION97.62
2.08-2.120.2231260.18392691X-RAY DIFFRACTION98.22
2.12-2.160.20411220.1742685X-RAY DIFFRACTION98.28
2.16-2.210.22691530.18242632X-RAY DIFFRACTION98.03
2.21-2.250.22541610.1762655X-RAY DIFFRACTION97.88
2.25-2.310.20851300.16752658X-RAY DIFFRACTION98.48
2.31-2.360.21381380.1652683X-RAY DIFFRACTION98.67
2.36-2.430.22011340.16522683X-RAY DIFFRACTION98.67
2.43-2.50.22421210.17352673X-RAY DIFFRACTION98.45
2.5-2.580.22231350.16672657X-RAY DIFFRACTION98.21
2.58-2.670.22641290.16432632X-RAY DIFFRACTION97.29
2.67-2.780.2011280.16862713X-RAY DIFFRACTION98.13
2.78-2.90.21591240.1742708X-RAY DIFFRACTION98.68
2.9-3.060.21211360.16812671X-RAY DIFFRACTION99.4
3.06-3.250.19591370.15352700X-RAY DIFFRACTION98.95
3.25-3.50.19551650.14112676X-RAY DIFFRACTION99.3
3.5-3.850.16891810.13722653X-RAY DIFFRACTION99.26
3.85-4.410.13961450.12472656X-RAY DIFFRACTION99.61
4.41-5.550.16711470.13442722X-RAY DIFFRACTION99.69
5.55-47.380.18581230.17352711X-RAY DIFFRACTION99.44

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