Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Isolated from human plasma vitronectin by CNBr cleavage
low
4.4
298
2
2D TOCSY
Isolated from human plasma vitronectin by CNBr cleavage
low
4.4
298
3
DQF-COSY
Isolated from human plasma vitronectin by CNBr cleavage
low
4.4
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
600
NMR Refinement
Method
Details
Software
simulated annealing
NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination.
Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4.
Discover
NMR Ensemble Information
Conformer Selection Criteria
structures with favorable non-bond energy
Conformers Calculated Total Number
60
Conformers Submitted Total Number
20
Representative Model
1 (closest to the average)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
structure solution
Discover
Discover 3 (2000)
Accelrys (San Diego, CA)
2
processing
Felix
Felix 2000
Accelrys (San Diego, CA)
3
data analysis
Sparky
Goddard, T.D. and Kneller, D.G.
4
data analysis
MOLMOL
Koradi, R., Billeter, M., and Wuthrich, K.
5
data analysis
PROCHECK
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R., and Thorntorn, J.M.