Activity and structure of EcoKMcrA.

Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M, Nucleic Acids Res 46(18):9829-9841 (2018) Europe PMC

SASDJY2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease

5-methylcytosine-specific restriction enzyme A (N-terminal domain)

MW^I(0)	21	kDa
MW^expected	21	kDa
V^Porod	29	nm³

log I(s) 1.24×10³ 1.24×10² 1.24×10¹ 1.24×10⁰

5-methylcytosine-specific restriction enzyme A (N-terminal domain) small angle scattering data

s, nm^-1

ln I(s)

5-methylcytosine-specific restriction enzyme A (N-terminal domain) Guinier plot

ln 1.25×10³ R_g: 2.1 nm 0 (2.1 nm)^-2 s²

(sR_g)²I(s)/I(0)

5-methylcytosine-specific restriction enzyme A (N-terminal domain) Kratky plot

1.104 0 √3 sR_g

p(r)	R_g: 2.2 nm 0 D_max: 7.5 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

0.5

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0.002
0.612

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

5-methylcytosine-specific restriction enzyme A (N-terminal domain) OTHER model

Synchrotron SAXS data from solutions of EcoKMcrA restriction endonuclease (N-terminal domain) in 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide, 1 mM DTT, were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.3 and 3.5 mg/ml were measured at 20°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Prone to aggregation

5-methylcytosine-specific restriction enzyme A (N-terminal domain) (EcoKMcrA-N)
Mol. type		Protein
Organism		Escherichia coli K-12
Olig. state		Monomer
Mon. MW		20.6 kDa

UniProt		P24200 (1-175)
Sequence		FASTA