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GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D IPAP [15N,1H]-HSQC
25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O
90% H2O/10% D2O
0.05
6.5
ambient
300
2
3D CT(H)CA(CO)NH
25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O
90% H2O/10% D2O
0.05
6.5
ambient
300
3
13C-COUPLED 3D HNCO
25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O
90% H2O/10% D2O
0.05
6.5
ambient
300
4
QUANTITATIVE J-CORRELATION 3D TROSY-HNCO
25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O
90% H2O/10% D2O
0.05
6.5
ambient
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX
600
2
Bruker
DRX
800
NMR Refinement
Method
Details
Software
simulated annealing
GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media (bicelle, peg, pf1 phage, negatively and positively charged polyacrylamide gels). Dipolar couplings originating on residues 10-11, 24-26, 39-41 and the n- and c-terminal residues were excluded, resulting in near-identity with the x-ray structure for these residues. This deposition corresponds to the refined-II structure of the primary citation that was refined against all 4 types of dipolar couplings in 5 media. The related depositions 1P7E and 1P7F correspond to the refined-III and refined-IV structures, respectively. The deposited structure was calculated with DYNAMO 2.1 following a short low-temperature molecular dynamics simulated annealing run starting from the regularized coordinates of the X-ray structure 1IGD using atomic coordinate restraints to the overlapping 3-residue segments of 1IGD. The force constants for the HN-N-C-Ca impropers were softened 10-fold relative to their standard settings. See the primary citation and the corresponding supporting information file for a detailed description of the refinement procedure. The deposited restraints file includes, in addition to the dipolar couplings and backbone H-bond distance restraints (XPLOR/CNS format), an Xplor-NIH script designed to mimic the deposited structure, and the force field parameter files. A set of overlapping 3-residue NCS restraint terms is used in this script in place of the Dynamo atomic coordinate restraints.