Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility

Area of Science:

• Structural biology
• X-ray crystallography
• Protein structure analysis

Background:

• Concanavalin A (ConA) is a well-studied protein with known biological functions.
• Previous atomic resolution structures of ConA exist, but variations have been observed.
• Understanding protein conformational flexibility is crucial for biological interpretation.

Purpose of the Study:

• To determine a high-resolution crystal structure of native concanavalin A (ConA).
• To investigate the conformational flexibility of ConA.
• To provide insights into the accuracy and precision of atomic resolution protein structures.

Main Methods:

• X-ray crystallography was used to determine the structure of ConA in a dimeric crystal form.
• High-resolution data collection to 1.56 A.
• Iterative model building and phase-bias removal using Shake&wARP for structure refinement.

Main Results:

• A new dimeric crystal structure of ConA was determined at 1.56 A resolution.
• The structure revealed differences in several regions compared to previously reported structures.
• Analysis of water-tyrosine interactions near the binding site suggests they are not unique to the active site.

Conclusions:

• The determined ConA structure provides new insights into its conformational flexibility.
• The study highlights potential substantial differences in local detail among precise structures of the same molecule.
• Recommendations are provided for representing ensembles of crystallographic models to improve interpretation of protein structures.