2XPH

Crystal structure of human SENP1 with the bound cobalt

Summary for 2XPH

• Entry DOI: 10.2210/pdb2xph/pdb
• Related: 2CKG 2CKH 2G4D 2IY0 2IY1 2IYC 2IYD 2XRE
• Descriptor: SENTRIN-SPECIFIC PROTEASE 1, GLYCEROL, COBALT (II) ION, ... (4 entities in total)
• Functional Keywords: hydrolase, cysteine protease, thiol protease
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Nucleus: Q9P0U3
• Total number of polymer chains: 2
• Total formula weight: 56774.21

Authors

Rimsa, V.,Eadsforth, T.,Hay, R.T.,Hunter, W.N. (deposition date: 2010-08-26, release date: 2010-09-08, Last modification date: 2023-12-20)

Primary citation

Rimsa, V.,Eadsforth, T.,Hay, R.T.,Hunter, W.N.
The Role of Co2+ in the Crystallization of Human Senp1 and Comments on the Limitations of Automated Refinement Protocols
Acta Crystallogr.,Sect.F, 67:442-, 2011

PubMed 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.

PubMed: 21505236
DOI: 10.1107/S1744309111005835

Experimental method

X-RAY DIFFRACTION (2.4 Å)