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- PDB-8k76: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 8k76
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum
ComponentsS-adenosylmethionine-dependent methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homologyMethyltransferase type 11 / Methyltransferase domain / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Methyltransferase
Function and homology information
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsHe, S.R. / Bai, X. / Zhang, J. / Zhao, Z.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum
Authors: He, S.R. / Bai, X.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine-dependent methyltransferase
B: S-adenosylmethionine-dependent methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,2252
Polymers57,2252
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-17 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.981, 80.629, 108.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S-adenosylmethionine-dependent methyltransferase


Mass: 28612.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN1919 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8R6D8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350,sodium citrate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.489→33 Å / Num. obs: 1036260 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.8
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 42568 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→33 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 4436 4.89 %
Rwork0.214 --
obs0.2146 90737 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 0 158 3821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.561
X-RAY DIFFRACTIONf_dihedral_angle_d6.236508
X-RAY DIFFRACTIONf_chiral_restr0.081578
X-RAY DIFFRACTIONf_plane_restr0.007662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.31441510.29792688X-RAY DIFFRACTION95
1.51-1.520.33971370.29232862X-RAY DIFFRACTION100
1.52-1.540.27661530.27442814X-RAY DIFFRACTION100
1.54-1.560.31791140.27282845X-RAY DIFFRACTION100
1.56-1.580.28231480.26272879X-RAY DIFFRACTION100
1.58-1.60.28341500.25182849X-RAY DIFFRACTION100
1.6-1.630.21511430.24012842X-RAY DIFFRACTION100
1.63-1.650.26571750.23792860X-RAY DIFFRACTION100
1.65-1.680.24041430.23152861X-RAY DIFFRACTION100
1.68-1.70.27381430.22022839X-RAY DIFFRACTION100
1.7-1.730.24871590.22152841X-RAY DIFFRACTION100
1.73-1.770.23141220.22832881X-RAY DIFFRACTION100
1.77-1.80.24861650.20942867X-RAY DIFFRACTION100
1.8-1.840.2461520.21632810X-RAY DIFFRACTION100
1.84-1.880.2131560.2062857X-RAY DIFFRACTION100
1.88-1.920.24581590.22042870X-RAY DIFFRACTION100
1.92-1.970.24571460.21912908X-RAY DIFFRACTION100
1.97-2.020.21231320.21242853X-RAY DIFFRACTION100
2.02-2.080.24381290.22142885X-RAY DIFFRACTION100
2.08-2.150.22481490.21732866X-RAY DIFFRACTION100
2.15-2.220.23091270.22432930X-RAY DIFFRACTION100
2.22-2.310.22341560.21032860X-RAY DIFFRACTION100
2.31-2.420.23611590.22142883X-RAY DIFFRACTION100
2.42-2.550.22341420.22932891X-RAY DIFFRACTION100
2.55-2.710.22851200.23412937X-RAY DIFFRACTION100
2.71-2.910.26331530.22882907X-RAY DIFFRACTION100
2.91-3.210.23951800.2342898X-RAY DIFFRACTION100
3.21-3.670.2181390.2052960X-RAY DIFFRACTION100
3.67-4.620.17741790.16912949X-RAY DIFFRACTION100
4.62-330.19081550.17793109X-RAY DIFFRACTION100

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