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PDBsum entry 1r6j
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Membrane protein
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PDB id
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1r6j
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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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The pdz2 domain of syntenin at ultra-High resolution: bridging the gap between macromolecular and small molecule crystallography.
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Authors
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B.S.Kang,
Y.Devedjiev,
U.Derewenda,
Z.S.Derewenda.
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Ref.
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J Mol Biol, 2004,
338,
483-493.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the second PDZ domain of the scaffolding protein
syntenin was solved using data extending to 0.73 A resolution. The
crystallographic model, including the hydrogen atoms and the anisotropic
displacement parameters, was refined to a conventional R-factor of 7.5% and
Rfree of 8.7%, making it the most precise crystallographic model of a protein
molecule to date. The model reveals discrete disorder in several places in the
molecule, and significant plasticity of the peptide bond, with some omega angles
deviating by nearly 20 degrees from planarity. Most hydrogen atoms are easily
identifiable in the electron density and weak hydrogen bonds of the C-H...O type
are clearly visible between the beta-strands. The study sets a new standard for
high-resolution protein crystallography.
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Figure 1.
Figure 1. Electron density maps around the disordered N
terminus of synPDZ2. The 2F[o] -F[c] electron density map (blue)
and F[o] -F[c] difference electron density map (red) from the
structure with major conformer alone are contoured at +4.0 s.
Major and minor conformers of residues Met194 to Arg197 are
shown as thick and thin frame, respectively. The Figures were
generated using O.[20.]
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Figure 4.
Figure 4. Examples of electron density maps revealing the
position of hydrogen atoms. The 2F[o] -F[c] electron density map
(gray) is contoured at +1.0 s, while the F[o] -F[c] difference
electron density map (red) prior to inclusion of hydrogen atoms
is contoured at +3.0 s and superimposed. A, Ile218; B, Lys203;
C, Leu258; and D, Ile247.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
338,
483-493)
copyright 2004.
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