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- PDB-8c9v: O-methyltransferase from Desulfuromonas acetoxidans -

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Basic information

Entry
Database: PDB / ID: 8c9v
TitleO-methyltransferase from Desulfuromonas acetoxidans
ComponentsO-methyltransferase, family 3
KeywordsTRANSFERASE
Function / homology
Function and homology information


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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-methyltransferase, family 3
Similarity search - Component
Biological speciesDesulfuromonas acetoxidans DSM 684 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhang, L. / Groves, M.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)893122European Union
CitationJournal: Chembiochem / Year: 2023
Title: Structural Characterization and Extended Substrate Scope Analysis of Two Mg 2+ -Dependent O-Methyltransferases from Bacteria.
Authors: Sokolova, N. / Zhang, L. / Deravi, S. / Oerlemans, R. / Groves, M.R. / Haslinger, K.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-methyltransferase, family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6662
Polymers22,6411
Non-polymers241
Water1,78399
1
A: O-methyltransferase, family 3
hetero molecules

A: O-methyltransferase, family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3324
Polymers45,2832
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1800 Å2
ΔGint-36 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.791, 44.791, 204.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein O-methyltransferase, family 3


Mass: 22641.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfuromonas acetoxidans DSM 684 (bacteria)
Gene: Dace_1119 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1JXV1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16% Glycerol; 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→44.79 Å / Num. obs: 34799 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 23
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.227 / Num. unique obs: 1667 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→43.796 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.17 / SU B: 3.745 / SU ML: 0.059 / Average fsc free: 0.9252 / Average fsc work: 0.9402 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2173 1706 4.918 %
Rwork0.1714 32981 -
all0.174 --
obs-34687 99.842 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.427 Å2-0 Å2-0 Å2
2--0.427 Å2-0 Å2
3----0.854 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 1 99 1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131476
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151401
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.6312004
X-RAY DIFFRACTIONr_angle_other_deg1.5081.5763210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7482280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4181511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined0.2260.2276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21311
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2742
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.212
X-RAY DIFFRACTIONr_nbd_other0.2870.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.26
X-RAY DIFFRACTIONr_mcbond_it2.6812.033746
X-RAY DIFFRACTIONr_mcbond_other2.6482.033745
X-RAY DIFFRACTIONr_mcangle_it3.1263.057929
X-RAY DIFFRACTIONr_mcangle_other3.1313.056930
X-RAY DIFFRACTIONr_scbond_it3.5782.335730
X-RAY DIFFRACTIONr_scbond_other3.5752.333731
X-RAY DIFFRACTIONr_scangle_it4.0323.3981075
X-RAY DIFFRACTIONr_scangle_other4.033.3971076
X-RAY DIFFRACTIONr_lrange_it3.94425.1731631
X-RAY DIFFRACTIONr_lrange_other3.93924.8631617
X-RAY DIFFRACTIONr_rigid_bond_restr4.34832875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3161320.2832371X-RAY DIFFRACTION99.8803
1.539-1.5810.2951200.212317X-RAY DIFFRACTION100
1.581-1.6270.2541030.1922267X-RAY DIFFRACTION99.8736
1.627-1.6770.2731290.1772199X-RAY DIFFRACTION99.9571
1.677-1.7320.241050.172144X-RAY DIFFRACTION100
1.732-1.7930.2431140.1552095X-RAY DIFFRACTION100
1.793-1.8610.2211120.1351981X-RAY DIFFRACTION99.9045
1.861-1.9360.2131060.141900X-RAY DIFFRACTION100
1.936-2.0230.229750.141890X-RAY DIFFRACTION100
2.023-2.1210.201950.151798X-RAY DIFFRACTION100
2.121-2.2360.211910.1421696X-RAY DIFFRACTION99.9441
2.236-2.3720.22840.1391621X-RAY DIFFRACTION100
2.372-2.5350.229730.1531526X-RAY DIFFRACTION100
2.535-2.7380.232630.1631430X-RAY DIFFRACTION100
2.738-30.188880.1711323X-RAY DIFFRACTION99.9292
3-3.3540.202510.1751221X-RAY DIFFRACTION100
3.354-3.8720.179480.1811082X-RAY DIFFRACTION99.297
3.872-4.7420.225480.157931X-RAY DIFFRACTION98.8889
4.742-6.7050.21470.214736X-RAY DIFFRACTION98.6146
Refinement TLS params.Method: refined / Origin x: 7.6281 Å / Origin y: 13.4845 Å / Origin z: 13.1814 Å
111213212223313233
T0.0816 Å2-0.0276 Å20.0283 Å2-0.0492 Å2-0.0012 Å2--0.0186 Å2
L1.9514 °20.3034 °2-0.0046 °2-1.8382 °20.0909 °2--2.2589 °2
S0.0807 Å °-0.1679 Å °0.0736 Å °0.3186 Å °-0.0438 Å °0.1719 Å °-0.0496 Å °-0.1734 Å °-0.037 Å °
Refinement TLS groupSelection: ALL

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