title: The role of Co²+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols.
abstract: 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.
authors.affiliation: Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.
authors.forename: Vadim
authors.initials: V
authors.lastname: Rimsa
authors.forename: Thomas
authors.initials: T
authors.lastname: Eadsforth
authors.forename: William N
authors.initials: WN
authors.lastname: Hunter
mesh_terms: D002413:Cations, Divalent / Q000737:chemistry; D003035:Cobalt / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D003546:Cysteine Endopeptidases; D030562:Databases, Protein; D010450:Endopeptidases / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D017434:Protein Structure, Tertiary
chemical_list: D002413:Cations, Divalent; D003035:Cobalt; D010450:Endopeptidases; C404512:SENP1 protein, human; D003546:Cysteine Endopeptidases