Solution Structure of the Enzyme I dimer Using Residual Dipolar Couplings and Small Angle X-Ray Scattering
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion
1
2
Scattering Type
x-ray
neutron
Radiation/Neutron Source
ALS
NIST NCNR
Synchrotron
Y
N
Beamline Type
2.12-IDC
30M NG3
Detector Type
Gold CCD
Detector Manufacturer Details
Temperature (K)
298
298
pH
7.4
7.4
Numer of Time Frames Used
20
Protein Concentration Range (mg/mL)
2.5-5
5
Sample Buffer
Data Reduction Software
Guiner Mean Radius Of Gyration (nm)
41.9
44.2
Sigma Mean Radius Of Gyration
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)
150
150
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
GNOM,XPLOR-NIH
PDB ENTRIES 2HWG AND 3EZA
99
1
REGULARIZED MEAN OF 99 MODELS
1
The initial structure of the EI dimer was constructed as a
hybrid of the crystal structure of phosphorylated EI
intermediate captured by the ...
The initial structure of the EI dimer was constructed as a
hybrid of the crystal structure of phosphorylated EI
intermediate captured by the inhibitor oxalate (PDB code
2HWG) and the NMR structure of the EIN-HPr complex (PDB code
3EZA). Throughout the structure determination, the backbone
atomic coordinates of each EIN domain (residues 1-254) were
treated as rigid bodies, with the two symmetry related EIC
domains (residues 262- 573) held fixed in space. Coordinates
in the linker region (residues 255-261) were allowed varying
degrees of freedom during the calculation through the use of
the internal variable module (IVM) of Xplor-NIH.
This entry corresponds to the regularized mean of the 99
structures for which data was reported in the primary
publication, with the B-factor column representing the per-atom
spread (in B-factor units). The calculated structural
statistics for the original 99 structures and for the
regularized mean are shown below.
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
TROSY-based 1H-15N correlation spectroscopy
20 mM TRIS, 100 mM sodium chloride, 10 mM DTT, 4 mM MgCl2, 1 mM EDTA, 10 % D2O, 1 tablet protease inhibitor, 0.15 mM EI dimer
90% H2O/10% D2O
7.4
ambient
310
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
800
NMR Refinement
Method
Details
Software
simulated annealing
STRUCTURE STATISTICS: MODEL 1: SAXS CHI2 Q->0.44: 0.43 SAXS CHI2 FULL RANGE: 2.26 SANS CHI2: 0.39 RDC R-FACTOR: 18.03 % RDC DA: 14.5 HZ RDC RH: 0.49 MODEL 2: SAXS CHI2 Q->0.44: 0.40 SAXS CHI2 FULL RANGE: 1.99 SANS CHI2: 0.58 RDC R-FACTOR: 18.07 RDC DA: 14.5 HZ RDC RH: 0.48 AVERAGE OVER THE FULL 99-MEMBER ENSEMBLE: SAXS CHI2 Q->0.44: 0.29 +/- 0.05 SAXS CHI2 FULL RANGE: 1.34 +/- 0.27 SANS CHI2: 0.41 +/- 0.08 RDC R-FACTOR: 18.07 +/- 0.02 % RDC DA: 14.5 +/- 0.1 HZ RDC RH: 0.49 +/- 0.00