5AZA

Crystal structure of MBP-sAglB fusion protein with a 20-residue spacer in the connector helix

Summary for 5AZA

• Entry DOI: 10.2210/pdb5aza/pdb
• Related: 5AZ6 5AZ7 5AZ8 5AZ9
• Related PRD ID: PRD_900001
• Descriptor: Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: fusion protein, sugar binding protein, transferase
• Biological source: Escherichia coli; More
• Total number of polymer chains: 1
• Total formula weight: 97502.34

Authors

Matsuoka, R.,Kohda, D. (deposition date: 2015-09-27, release date: 2016-01-13, Last modification date: 2024-10-23)

Primary citation

Matsuoka, R.,Shimada, A.,Komuro, Y.,Sugita, Y.,Kohda, D.
Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.
Protein Sci., 25:754-768, 2016

PubMed Abstract: Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.

PubMed: 26694222
DOI: 10.1002/pro.2867

Experimental method

X-RAY DIFFRACTION (2.08 Å)