2L5H | pdb_00002l5h

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

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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 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	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		Xplor-NIH

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	120
Conformers Submitted Total Number	2
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Xplor-NIH	2.25	Schwieters, Kuszewski, Tjandra and Clore
2	refinement	Xplor-NIH	2.25	Schwieters, Kuszewski, Tjandra and Clore