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- PDB-8xdq: O-methyltransferase from Lycoris aurea complexed with Mg and SAH -

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Basic information

Entry
Database: PDB / ID: 8xdq
TitleO-methyltransferase from Lycoris aurea complexed with Mg and SAH
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / O-methyltransferase family protein / LaOMT
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesLycoris aurea (golden spider-lily)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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)56,06210
Polymers54,8472
Non-polymers1,2168
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-43 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.766, 81.374, 119.205
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 spider-lily) / Production host: Escherichia coli M15 (bacteria)

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Non-polymers , 5 types, 420 molecules

#2: 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
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 23% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 7.0)

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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: 1.77→48.08 Å / Num. obs: 91013 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 20.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.9
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.084 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2683 / CC1/2: 0.785 / % 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: 1.77→48.08 Å / SU ML: 0.1777 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.0397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 4562 5.01 %
Rwork0.1618 86451 -
obs0.1632 91013 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.82 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 20 412 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644181
X-RAY DIFFRACTIONf_angle_d0.86935707
X-RAY DIFFRACTIONf_chiral_restr0.0532637
X-RAY DIFFRACTIONf_plane_restr0.0047738
X-RAY DIFFRACTIONf_dihedral_angle_d17.9087612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.30971560.26822810X-RAY DIFFRACTION100
1.79-1.810.31391240.25532883X-RAY DIFFRACTION99.9
1.81-1.830.26831460.24822954X-RAY DIFFRACTION99.9
1.83-1.860.28091260.24142881X-RAY DIFFRACTION99.93
1.86-1.880.27811440.23052835X-RAY DIFFRACTION99.9
1.88-1.910.23181530.22122986X-RAY DIFFRACTION99.9
1.91-1.930.29821710.20982803X-RAY DIFFRACTION99.8
1.93-1.960.23051870.20482828X-RAY DIFFRACTION100
1.96-1.990.25581360.20022972X-RAY DIFFRACTION99.81
1.99-2.030.23111430.19372848X-RAY DIFFRACTION99.93
2.03-2.060.22321450.18132903X-RAY DIFFRACTION99.93
2.06-2.10.25871600.17782900X-RAY DIFFRACTION99.9
2.1-2.140.16951570.16122837X-RAY DIFFRACTION99.97
2.14-2.180.19381910.16262881X-RAY DIFFRACTION100
2.18-2.230.18951160.15762895X-RAY DIFFRACTION100
2.23-2.280.19911620.15772901X-RAY DIFFRACTION100
2.28-2.340.19721570.15672886X-RAY DIFFRACTION99.93
2.34-2.40.16091490.15342869X-RAY DIFFRACTION99.93
2.4-2.470.17531480.15372905X-RAY DIFFRACTION99.97
2.47-2.550.18411690.16132815X-RAY DIFFRACTION99.8
2.55-2.640.21241590.15242896X-RAY DIFFRACTION99.41
2.64-2.750.18941160.14892884X-RAY DIFFRACTION99.57
2.75-2.870.17271630.1562906X-RAY DIFFRACTION99.93
2.88-3.030.18471380.15922888X-RAY DIFFRACTION99.93
3.03-3.220.18091450.15012886X-RAY DIFFRACTION99.97
3.22-3.460.17781900.142864X-RAY DIFFRACTION99.93
3.46-3.810.14791410.13652915X-RAY DIFFRACTION99.93
3.81-4.360.12421830.12722830X-RAY DIFFRACTION99.93
4.36-5.50.18111340.14092906X-RAY DIFFRACTION99.97
5.5-48.080.21131530.17592884X-RAY DIFFRACTION99.7

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