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.
SOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDROPHOBIC RESIDUES TYPICAL OF A VL/VH INTERFACE
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
3D combined 13C/15N-separated NOESY
10mM sodium phosphate
150mM NaCl
0.2mM EDTA
90% H2O/10% D2O
0.16
6.8
1 atm
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
800
NMR Refinement
Method
Details
Software
simulated annealing using
torsion angle and cartesian
dynamics
NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE
INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING
RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS
AN ASSIGNMENT FILTER TO REDUCE THE AMBIGUITY OF THE OTHER RESTRAINTS. THE
RESTRAINT LIST AND STRUCTURES WERE FURTHER REFINED BY MANUALLY CHOOSING
POSSIBILITIES FROM THE RESTRAINTS WITH LOW AMBIGUITY (BASED ON THE
SPECTRA).
NMRPipe
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
150
Conformers Submitted Total Number
10
Representative Model
1 (lowest energy)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
processing
NMRPipe
Frank Delaglio, Stephan Grzesiek, Ad Bax, Geerten W. Vuister, Guang Zhu, John Pfeifer
2
data analysis
NMRView
4.1.2
Bruce Johnson and Richard Blevins
3
structure solution
ARIA
1.0
J. Linge and M. Nilges
4
structure solution
CNS
1.0
AT Brunger, PD Adams, GM Clore, WL DeLano, P Gros, RW Grosse-Kunstleve, JS Jiang, J Kuszewski, M Nilges, NS Pannu, RJ Read, LM Rice, T Simonson, GL Warren