Small angle X-ray scattering as a complementary tool for high-throughput structural studies.

Grant TD, Luft JR, Wolfley JR, Tsuruta H, Martel A, Montelione GT, Snell EH, Biopolymers 95(8):517-30 (2011) Europe PMC

SASDCH6 – GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a

Diguanylate cyclase
MWexperimental 19 kDa
MWexpected 20 kDa
VPorod 32 nm3
log I(s) 1.01×103 1.01×102 1.01×101 1.01×100
Diguanylate cyclase small angle scattering data  s, nm-1
ln I(s)
Diguanylate cyclase Guinier plot ln 1.01×103 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
Diguanylate cyclase Kratky plot 1.104 0 √3 sRg
p(r)
Diguanylate cyclase pair distance distribution function Rg: 1.9 nm 0 Dmax: 6.6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Diguanylate cyclase PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Diguanylate cyclase DAMFILT model
Synchrotron SAXS data from solutions of GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a in 5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) storage ring (Menlo Park, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.13 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.9 and 6.1 mg/ml were measured at 20°C. 20 successive 1 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.

Diguanylate cyclase
Mol. type   Protein
Organism   Marinobacter hydrocarbonoclasticus
Olig. state   Monomer
Mon. MW   20.2 kDa
 
UniProt   A1U3W3
Sequence   FASTA
 
PDB ID   3IGN