Date Published: October 01, 2016
Publisher: International Union of Crystallography
Author(s): Wouter G. Touw, Bart van Beusekom, Jochem M. G. Evers, Gert Vriend, Robbie P. Joosten.
A method is presented to automatically validate and correct Zn–CysxHisy complexes that have a distorted tetrahedral geometry.
Many efforts have been directed towards improving the identification of ion types in macromolecular structures (see, for example, Sodhi et al., 2004 ▸; Hsin et al., 2008 ▸; Andreini et al., 2009 ▸, 2013 ▸; Hemavathi et al., 2010 ▸; Brylinski & Skolnick, 2011 ▸; Echols et al., 2014 ▸; Zheng et al., 2014 ▸; He et al., 2015 ▸; Morshed et al., 2015 ▸). The geometry of ion-binding sites often needs to be improved as well. The bond-valence method (Brown & Altermatt, 1985 ▸; Brese & O’Keeffe, 1991 ▸; Brown, 2009 ▸) that is generally used to identify ion types (Hooft, Vriend et al., 1996 ▸; Nayal & Di Cera, 1996 ▸; Müller et al., 2003 ▸; Zheng et al., 2014 ▸) requires that the modelled geometry of the binding site accurately represents the crystallographic data.
The geometry of both moderately and severely distorted ZnCysxHisy sites in the PDB could be improved substantially by restraining the sites to tetrahedral coordination geometry using both Zn–ligand distance restraints and tetrahedral Sγ—Zn—Sγ angle restraints. Correcting geometry using refinement with restraints based on prior chemical knowledge and validating the results require that accurate refinement targets are known. Geometric trends in systematically re-refined ZnCysxHisy sites show that current restraint targets may be replaced by context-specific targets. Context-specific angle restraint targets will soon be implemented in PDB_REDO and context-specific distance targets will follow subject to the availability of a suitable framework for these in REFMAC. Geometric targets for ZnCysxHisy sites may be further detailed once sufficient data are available.
The functionality to improve the refinement of ZnCysxHisy sites is available through the PDB_REDO web server (Joosten et al., 2014 ▸). Zen is distributed with PDB_REDO and the source code is available upon request. The WHAT IF web servers and web services are freely available and WHAT IF is shareware. WHAT_CHECK and PDB_REDO will become part of the CCP4 software suite (Winn et al., 2011 ▸) soon. A large .csv file that contains all of the data used for analysing the 8435 tetrahedral ZnCysxHisy complexes is available as supplementary data.
The following references are cited in the Supporting Information for this article: Chung et al. (2005 ▸), Duan et al. (2009 ▸), Harding (2006 ▸), LaPlante et al. (2014 ▸), Ma et al. (2015 ▸), Samara et al. (2012 ▸) and Tamames et al. (2007 ▸).