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Solution structure of lactam analogue (DapE) of HIV gp41 600-612 loop.
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
3 mM peptide in 500 ul DMSO-D6
100% DMSO-D6
ambiant
298
2
DQF-COSY
3 mM peptide in 500 ul DMSO-D6
100% DMSO-D6
ambiant
298
3
TOCSY
3 mM peptide in 500 ul DMSO-D6
100% DMSO-D6
ambiant
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
Torsion angle dynamics, molecular dynamics, energy minimization.
50 initial random structure were generatd in DYANA software , followed by 500 ps restrained minimization + 35 ps MD in vacuo at 300K, 200 ps under NMR restraints and 750ps conjugated gradient EM using the DISCOVER module of MSI software
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
all calculated structures submitted
Conformers Calculated Total Number
50
Conformers Submitted Total Number
50
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
The structure was determined using standard 2D homonuclear techniques. Different NOESY experiments , with mixing times from 80 ms to 800 ms , were recorded in order to determined the best conditions avoiding spin diffusion.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
XwinNMR
2.6
Bruker GMBH
2
processing
XwinNMR
2.6
Bruker GMBH
3
data analysis
XEASY
1.2
Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR , 5, 1-10
4
refinement
DYANA
1.5
Guentert P., Mumethaler C.and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298