1P7E

GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: Best agreement with dipolar constraints 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy.

Ulmer, T.S.Ramirez, B.E.Delaglio, F.Bax, A.

(2003) J.Am.Chem.Soc. 125: 9179-9191

  • DOI: 10.1021/ja0350684
  • Primary Citation of Related Structures:  1P7F, 2OED

  • PubMed Abstract: 
  • NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besi ...

    NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity ( = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.


    Related Citations: 
    • THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G. AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB.
      Derrick, J.P.,Wigley, D.B.
      (1994) J.Mol.Biol. 243: 906


    Organizational Affiliation

    Contribution from the Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G binding protein G
A
56Streptococcus sp. group GGene Names: spg
Find proteins for P19909 (Streptococcus sp. group G)
Go to UniProtKB:  P19909
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: Best agreement with dipolar constraints 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance