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PDBsum entry 2omn
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Immune system
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PDB id
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2omn
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References listed in PDB file
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Key reference
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Title
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Bence jones kwr protein structures determined by X-Ray crystallography.
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Authors
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D.L.Makino,
A.H.Henschen-Edman,
S.B.Larson,
A.Mcpherson.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2007,
63,
780-792.
[DOI no: ]
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PubMed id
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Abstract
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A Bence Jones protein isolated in the early 1960s from a patient (initials KWR)
suffering from plasma-cell dyscrasia was crystallized and its structure was
analyzed in four different unit cells by X-ray diffraction. The final models of
the molecule in all crystal forms were virtually the same, although the elbow
angles relating the constant and variable domains of the Bence Jones dimers
varied over a range of 10 degrees. The tetragonal form had an R factor of 22.6%
and an R(free) of 28.3% at 2.2 A resolution. Phosphate or sulfate ions
(depending on the crystallization conditions) were found in the
antigen-combining sites in all crystals, as well as an unidentified ligand
tightly bound in the hydrophobic 'deep pocket' beneath the antigen-binding site.
The ligand was treated as a phenol molecule. Two trigonal crystal forms were
among those solved. One was grown at pH 4.0 and the other was only obtained
after sitting for more than eight months at room temperature. The latter crystal
was composed of molecules that were degraded in their constant domains. Both low
pH and proteolytic degradation of constant domains are known to promote the
polymerization of some Bence Jones proteins into amyloid fibrils. Indeed, in
both trigonal crystal forms the molecules are organized with pseudo-hexagonal
symmetry about the unique crystallographic axes in a manner suggestive of such
fibrils. The arrangement of Bence Jones dimers is also consistent with other
observations regarding Bence Jones amyloid-fibril structure and current models.
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Figure 6.
Figure 6 Sulfate-ion and phosphate-ion interactions in the main
cavity of what would be the antigen-binding site of a Fab. The
elbow region of the P3[2]21 crystal shows the location of the
phenol molecule and a phosphate also observed in that region. A
symmetry-related molecule is indicated in gray.
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Figure 8.
Figure 8 Detail of the lateral interactions between neighboring
variable domains in the P3[1]21 crystal. (a) Interaction between
adjacent  -strands
from two variable domains of chains B and D forms an extended
-sheet;
(b) lateral interactions between neighboring variable domains of
chains A and C.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2007,
63,
780-792)
copyright 2007.
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