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PDBsum entry 1rb5
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DNA binding protein
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PDB id
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1rb5
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Automated protein crystal structure determination using elves.
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Authors
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J.Holton,
T.Alber.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
1537-1542.
[DOI no: ]
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PubMed id
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Abstract
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Efficient determination of protein crystal structures requires automated x-ray
data analysis. Here, we describe the expert system ELVES and its use to
determine automatically the structure of a 12-kDa protein. Multiwavelength
anomalous diffraction analysis of a selenomethionyl derivative was used to image
the Asn-16-Ala variant of the GCN4 leucine zipper. In contrast to the parallel,
dimeric coiled coil formed by the WT sequence, the mutant unexpectedly formed an
antiparallel trimer. This structural switch reveals how avoidance of core
cavities at a single site can select the native fold of a protein. All structure
calculations, including indexing, data processing, locating heavy atoms, phasing
by multiwavelength anomalous diffraction, model building, and refinement, were
completed without human intervention. The results demonstrate the feasibility of
automated methods for determining high-resolution, x-ray crystal structures of
proteins.
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Figure 2.
Fig. 2. Experimental, 1.8-Å resolution MAD-phased
electron density map (P3[1]21, contoured at 1  )
produced by ELVES superimposed on the refined model of the GCN4
Asn-16-Ala leucine-zipper variant. (A) Cross section through the
trimer at the level of the Ala-16-Leu-12-Leu-12 layer. (B) Cross
section through the trimer at the level of the
Leu-12-Ala-16-Ala-16 layer.
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Figure 3.
Fig. 3. The Asn-16-Ala variant of the GCN4 leucine zipper
forms an antiparallel, trimeric coiled coil. (A) Stereo ribbon
diagram of the overall structure. Each helix is colored in
increasingly cool colors from the amino to the carboxyl
terminus. (B) Superpositions of the structures determined by
automated (blue) and manual (yellow) methods in the trigonal
(Left) and tetragonal (Right) crystal forms. (C) Cross section
showing the Ala-16-Leu-12-Leu-12 layer with the van der Waals
surfaces of the core amino acids filling the space in the core
of the trimer. (D) Close packing of the Leu-12-Ala-16-Ala-16
layer. (E) In contrast, a 165-Å3 cavity exists in the
Ala-16 layer of the parallel trimer stabilized by benzene (29).
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Secondary reference #1
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Title
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An engineered allosteric switch in leucine-Zipper oligomerization.
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Authors
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L.Gonzalez,
J.J.Plecs,
T.Alber.
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Ref.
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Nat Struct Biol, 1996,
3,
510-515.
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PubMed id
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Secondary reference #2
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Title
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Crystal structure of an isoleucine-Zipper trimer.
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Authors
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P.B.Harbury,
P.S.Kim,
T.Alber.
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Ref.
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Nature, 1994,
371,
80-83.
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PubMed id
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Secondary reference #3
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Title
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A switch between two-, Three-, And four-Stranded coiled coils in gcn4 leucine zipper mutants.
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Authors
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P.B.Harbury,
T.Zhang,
P.S.Kim,
T.Alber.
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Ref.
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Science, 1993,
262,
1401-1407.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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X-Ray structure of the gcn4 leucine zipper, A two-Stranded, Parallel coiled coil.
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Authors
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E.K.O'Shea,
J.D.Klemm,
P.S.Kim,
T.Alber.
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Ref.
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Science, 1991,
254,
539-544.
[DOI no: ]
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PubMed id
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