The PDZ2 domain of syntenin at ultra-high resolution: Bridging the gap between macromolecular and small molecule crystallography

Beom Sik Kang, Yancho Devedjiev, Urszula Derewenda, Zygmunt S. Derewenda

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73Å 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 ω angles deviating by nearly 20°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 β-strands. The study sets a new standard for high-resolution protein crystallography.

Original languageEnglish
Pages (from-to)483-493
Number of pages11
JournalJournal of Molecular Biology
Volume338
Issue number3
DOIs
StatePublished - 30 Apr 2004

Keywords

  • Crystallography
  • LHB, lost hydrogen bond
  • PDZ
  • PEG, polyethylene glycol
  • Syntenin
  • Ultra-high resolution

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