3W9V

Crystal structure of refolded DING protein

Summary for 3W9V

• Entry DOI: 10.2210/pdb3w9v/pdb
• Related: 2Q9T 2V3Q 3G62 3W9W
• Descriptor: Phosphate-binding protein, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: ding, refolded, phosphate binding apolipoprotein, phosphate, transport protein
• Biological source: unidentified prokaryotic organism
• Cellular location: Secreted : P85173
• Total number of polymer chains: 2
• Total formula weight: 77812.61

Authors

Gai, Z.Q.,Nakamura, A.,Tanaka, Y.,Hirano, N.,Tanaka, I.,Yao, M. (deposition date: 2013-04-17, release date: 2013-10-30, Last modification date: 2024-11-06)

Primary citation

Gai, Z.Q.,Nakamura, A.,Tanaka, Y.,Hirano, N.,Tanaka, I.,Yao, M.
Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation.
J.SYNCHROTRON RADIAT., 20:854-858, 2013

PubMed Abstract: After crystallization of a certain protein-RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.

PubMed: 24121327
DOI: 10.1107/S0909049513020694

Experimental method

X-RAY DIFFRACTION (1.031 Å)