1JJZ

REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY5 mM kalata B1; 90% H2O, 10% D2O90% H2O/10% D2O03ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDMX750
NMR Refinement
MethodDetailsSoftware
torsion angle dynamicsStructures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide bond cyclizing the peptide backbone. Residue numbering follows the original description of citation 1, except that for the purposes of structure calculations, the N-terminal residue was taken as Asn8. Therefore, residues 30-36 in this deposition correspond to residues 1-7 in citation 1 and related PDB entry 1kal. Structures were refined in the absence of any artificial constraints defining disulfide bonds until all NOEs had been assigned and low target functions were achieved (tf=0.6). 15 additional calculations were performed with these input data and the inclusion of constraints defining all possible disulfide pairing combinations. The structures containing disulfides between [5(34)-13], [17-29] and [22-27] displayed the lowest target function (0.74, second lowest was 1.54). On the basis of this result and analysis of NOEs observed between Cys sidechain protons, this disulfide bonding arrangement was assumed to be correct and served as the basis for this deposition.DYANA
NMR Ensemble Information
Conformer Selection Criteriatarget function
Conformers Calculated Total Number50
Conformers Submitted Total Number20
Additional NMR Experimental Information
DetailsStructure was determined using NOEs from a single 100 ms mixing time NOESY experiment
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementDYANA1.5P. Guentert
2collectionXwinNMR2.6Bruker
3data analysisXEASY1.3.11C. Bartels