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PDBsum entry 1jml
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Protein binding
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PDB id
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1jml
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References listed in PDB file
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Key reference
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Title
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Conversion of monomeric protein l to an obligate dimer by computational protein design.
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Authors
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B.Kuhlman,
J.W.O'Neill,
D.E.Kim,
K.Y.Zhang,
D.Baker.
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Ref.
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Proc Natl Acad Sci U S A, 2001,
98,
10687-10691.
[DOI no: ]
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PubMed id
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Abstract
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Protein L consists of a single alpha-helix packed on a four-stranded beta-sheet
formed by two symmetrically opposed beta-hairpins. We use a computer-based
protein design procedure to stabilize a domain-swapped dimer of protein L in
which the second beta-turn straightens and the C-terminal strand inserts into
the beta-sheet of the partner. The designed obligate dimer contains three
mutations (A52V, N53P, and G55A) and has a dissociation constant of
approximately 700 pM, which is comparable to the dissociation constant of many
naturally occurring protein dimers. The structure of the dimer has been
determined by x-ray crystallography and is close to the in silico model.
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Figure 3.
Fig. 3. Simulated annealing composite omit map (2F[obs]
 F[calc])
of the VPA hinge region. The mutated residues (V52, P53, and
A55) are highlighted in yellow. The electron density was
contoured at 1  .
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Figure 5.
Fig. 5. Comparison of the VPA design model to the VPA
crystal structure. (A) Shown in blue (asymmetric unit) and cyan
(symmetry mate) are the two halves that constitute the VPA
crystal structure, and in dark and light orange is the modeled
VPA (based on the G55A structure). The overall main-chain rms
deviation is 0.40 Å for the blue and orange structures.
(B) A close-up of the mutated region.
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