Open AccessThe role of Co 2+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols
Author(s) -
Rimsa Vadim,
Eadsforth Thomas,
Hunter William N.
Publication year - 2011
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
ISSN - 1744-3091
DOI - 10.1107/s1744309111005835
Subject(s) - crystallization , crystallography , intermolecular force , molecule , macromolecule , chemical physics , ion , divalent , protein crystallization , materials science , chemistry , biochemistry , organic chemistry
Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium‐resolution electron‐density map of the catalytic domain of human sentrin‐specific protease 1 (SENP1), a strong feature indicative of an ordered divalent cation was noted. This was assigned as Co 2+ , an essential component of the crystallization mixture. The ion displays tetrahedral coordination by Glu430 and His640 from one molecule and the corresponding residues from a symmetry‐related molecule. Analysis of the data derived from a previous structure of SENP1 suggested that Co 2+ had been overlooked and re‐refinement supported this conclusion. High‐throughput automated re‐refinement protocols also failed to mark the Co 2+ position, supporting the requirement for the incorporation of as much information as possible to enhance the value of such protocols.