Solution Structure of the H189Q mutant of the Enzyme I dimer Using Residual Dipolar Couplings and Small Angle X-Ray Scattering
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion
1
Scattering Type
x-ray
Radiation/Neutron Source
APS
Synchrotron
Y
Beamline Type
12-IDC
Detector Type
Gold CCD
Detector Manufacturer Details
ECT division, Argonne National Laboratory
Temperature (K)
298
pH
7.4
Numer of Time Frames Used
20
Protein Concentration Range (mg/mL)
5
Sample Buffer
20 mM Tris, 100 mM NaCl, 10 mM DTT, 4 mM MgCl2, 1 mM EDTA, 1 tablet protease inhibitor cocktail (SigmaFAST S8830)
Data Reduction Software
Mar_Detector, Igor, Primus, Gnom
Guiner Mean Radius Of Gyration (nm)
4.1
Sigma Mean Radius Of Gyration
0.1
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)
15.5
Solution Scattering Data Analysis and Model Fitting
Method
Software
Software Authors
Starting Model
Conformers, Number Calculated
Conformers, Number Submitted
Conformers, Selection Criteria
Best Representative Conformer
Other Details
simulated annealing
XPLOR-NIH
C.D. Schwieters, J.J. Kuszewski, N. Tjandra,G.M. Clore
free wildtype EI structures, PDB ID 2KX9
120
2
lowest energy
1
The initial structure of the H189Q mutant of the EI dimer was taken from the calculated structures of the wildtype EI dimer summarized in PDB entry 2K ...
The initial structure of the H189Q mutant of the EI dimer was taken from the calculated structures of the wildtype EI dimer summarized in PDB entry 2KX9. Throughout the structure determination, the backbone atomic coordinates of the c-terminus of each EI subunit (residues 262-573) were held fixed in space, while the two subdomains of each n-terminus (residues 25-142 in the alpha subdomain, and residues 1-21 and 147-254 in the alpha-beta subdomain) were treated as rigid bodies. Coordinates in the linker regions (residues 22-24, 143-146, and 255-261) and interfactial sidechains were allowed varying degrees of freedom during the calculation through the use of the internal variable module (IVM) of Xplor-NIH. Model 1 corresponds to the regularized mean of the 100 structures for which data was reported in the primary publication, with the B-factor column representing the per-atom spread (in B-factor units). Model 2 is the lowest energy structure. The calculated structural statistics for the original 96 structures and for the two reported structures are: MODEL 1: SAXS CHI2 Q->0.44: 0.63 SAXS CHI2 FULL RANGE: 0.80 RDC R-FACTOR: 18.76 RDC DA: 11.16 RDC RH: 0.59 MODEL 2: SAXS CHI2 Q->0.44: 0.50 SAXS CHI2 FULL RANGE: 0.72 RDC R-FACTOR: 19.18 RDC DA: 11.15 RDC RH: 0.60 AVERAGE OVER THE FULL 99-MEMBER ENSEMBLE: SAXS CHI2 Q->0.44: 0.58 +/- 0.10 SAXS CHI2 FULL RANGE: 0.76 +/- 0.16 RDC R-FACTOR: 19.02 +/- 0.37 RDC DA: 11.13+/- 0.19 RDC RH: 0.59 +/- 0.02
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
TROSY-based 1H-15N correlation spectroscopy
20 mM TRIS-1, 100 mM sodium chloride-2, 10 mM DTT-3, 4 mM MgCl2-4, 1 mM EDTA-5, 10 % D2O-6, 0.15 mM EI dimer-8
