1BDD

STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 55 
  • Conformers Submitted: 
  • Selection Criteria: AT FIRST, THE DEPOSITORS CARRIED OUT THE DISTANCE GEOMETRY CALCULATION BY STARTING FROM 55 INITIAL STRUCTURES. THIS CALCULATION RESULTED IN 41 SOLUTIONS, WHICH HAD CORRECT POLYPEPTIDE FOLDS EXCLUDING 14 MIRROR-IMAGE SUBSTRUCTURES. NEXT, THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE PERFORMED BY USING THESE 41 SUBSTRUCTURES. THE DISTANCE AND TORSION ANGLE VIOLATIONS OF THE 41 SOLUTIONS OBTAINED BY THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE SMALLER THAN 0.6 ANGSTROMS AND 27 DEGREES, RESPECTIVELY. THE DEPOSITORS SELECTED 10 SOLUTIONS THAT HAD THE DISTANCE AND TORSION ANGLE VIOLATIONS OF SMALLER THAN 0.5 ANGSTROMS AND 10 DEGREES, RESPECTIVELY. 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

Gouda, H.Torigoe, H.Saito, A.Sato, M.Arata, Y.Shimada, I.

(1992) Biochemistry 31: 9665-9672

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional solution structure of the recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G, was determined by NMR spectroscopy and hybrid distance geometry-dynamical simulated ...

    The three-dimensional solution structure of the recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G, was determined by NMR spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. On the basis of 692 experimental constraints including 587 distance constraints obtained from the nuclear Overhauser effect (NOE), 57 torsion angle (phi, chi 1) constraints, and 48 constraints associated with 24 hydrogen bonds, a total of 10 converged structures of FB were obtained. The atomic root mean square difference among the 10 converged structures is 0.52 +/- 0.10 A for the backbone atoms and 0.98 +/- 0.08 A for all heavy atoms (excluding the N-terminal segment from Thr1 to Glu9 and the C-terminal segment from Gln56 to Ala60, which are partially disordered). FB is composed of a bundle of three alpha-helices, i.e., helix I (Gln10-His19), helix II (Glu25-Asp37), and helix III (Ser42-Ala55). Helix II and helix III are antiparallel to each other, whereas the long axis of helix I is tilted at an angle of about 30 degrees with respect to those of helix II and helix III. Most of the hydrophobic residues of FB are buried in the interior of the bundle of the three helices. It is suggested that the buried hydrophobic residues form a hydrophobic core, contributing to the stability of FB.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Sequential 1H NMR Assignments and Secondary Structure of the B Domain of Staphylococcal Protein A: Structural Changes between the Free B Domain in Solution and the Fc-Bound B Domain in Crystal
      Torigoe, H.,Shimada, I.,Saito, A.,Sato, M.,Arata, Y.
      (1990) Biochemistry 29: 8787
    • 15N Nuclear Magnetic Resonance Studies of the B Domain of Staphylococcal Protein A: Sequence Specific Assignments of the Imide 15N Resonances of the Proline Residues and the Interaction with Human Immunoglobulin G
      Torigoe, H.,Shimada, I.,Waelchli, M.,Saito, A.,Sato, M.,Arata, Y.
      (1990) FEBS Lett. 269: 174
    • High Level Expression of a Synthetic Gene Coding for Igg-Binding Domain B of Staphylococcal Protein A
      Saito, A.,Honda, S.,Nishi, T.,Koike, M.,Okazaki, K.,Itoh, S.,Sato, M.
      (1989) Protein Eng. 2: 481


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STAPHYLOCOCCUS AUREUS PROTEIN A
A
60Staphylococcus aureusMutation(s): 0 
Gene Names: spa
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 55 
  • Conformers Submitted: 
  • Selection Criteria: AT FIRST, THE DEPOSITORS CARRIED OUT THE DISTANCE GEOMETRY CALCULATION BY STARTING FROM 55 INITIAL STRUCTURES. THIS CALCULATION RESULTED IN 41 SOLUTIONS, WHICH HAD CORRECT POLYPEPTIDE FOLDS EXCLUDING 14 MIRROR-IMAGE SUBSTRUCTURES. NEXT, THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE PERFORMED BY USING THESE 41 SUBSTRUCTURES. THE DISTANCE AND TORSION ANGLE VIOLATIONS OF THE 41 SOLUTIONS OBTAINED BY THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS WERE SMALLER THAN 0.6 ANGSTROMS AND 27 DEGREES, RESPECTIVELY. THE DEPOSITORS SELECTED 10 SOLUTIONS THAT HAD THE DISTANCE AND TORSION ANGLE VIOLATIONS OF SMALLER THAN 0.5 ANGSTROMS AND 10 DEGREES, RESPECTIVELY. 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance