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PDBsum entry 1edj
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Immunoglobulin-binding protein
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PDB id
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1edj
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References listed in PDB file
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Key reference
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Title
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Solution structure of the e-Domain of staphylococcal protein a.
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Authors
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M.A.Starovasnik,
N.J.Skelton,
M.P.O'Connell,
R.F.Kelley,
D.Reilly,
W.J.Fairbrother.
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Ref.
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Biochemistry, 1996,
35,
15558-15569.
[DOI no: ]
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PubMed id
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Abstract
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The E-domain of staphylococcal protein A is one of five homologous IgG-binding
domains designated E, D, A, B, and C that comprise the extracellular portion of
protein A. The E-domain binds tightly to Fc fragments of IgG and binds certain
Fv fragments with micromolar affinity. To explore further the structural
features of Fc binding by protein A, and as a first step in developing a
structural understanding of E-domain/Fv complex formation, we have determined
the solution structure of the uncomplexed E-domain using 2D homonuclear and
heteronuclear NMR spectroscopy. Complete 1H and 15N resonance assignments were
obtained, and the structure was determined from 383 NOE-derived distance
restrains, 34 phi and 19 chi 1 dihedral angle restraints, and 54 restraints for
27 H-bonds. 3JH alpha-H beta coupling constants and long-range NOEs involving
Phe11 indicate the side chain exists in more than one conformation with
differing chi 1 values. NOE restraints that were incompatible with chi 1 = -60
degrees were removed from one set of structure calculations, and those
incompatible with chi 1 = 180 degrees were removed from a second set to allow
Phe11 to explore both rotamer wells. Thus, two sets of 20 final structures,
having no distance or dihedral angle restraint violations greater than 0.12 A or
1.6 degrees, respectively, represent the solution structure of the E-domain.
Backbone atomic rms differences with respect to the mean coordinates for each
set of 20 structures for residues 8-53 averaged 0.41 +/- 0.06 and 0.35 +/- 0.06
A. No significant differences in the overall structure result from the different
orientations of Phe11. The solution structure of the E-domain consists of three
alpha-helices that pack together to form a compact helical bundle. A detailed
comparison between the E-domain ensembles and the previously determined
structure for the B-domain in complex with Fc indicates that only the 180
degrees chi 1 rotamer of Phe11 is competent for binding; the -60 degrees chi 1
rotamer must reorient to 180 degrees to create a cavity that is filled by Ile253
from the CH2 domain of Fc in the Fc-bound complex.
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