Fig. 6

Flexibility and catalytic cavity volume fluctuations in the XynA domain. a Time series analysis of the catalytic cavity volume for the XynA domain in the parental XynA (light gray dashed line), the 2091A (open, xylose-free, dark gray line) and 2621B (open, xylose-free, black line). b Conformational fluctuations of XynA domain in 2091A (gray) and 2621B (black) without xylose (dashed line) and with xylose (solid line). The root mean square fluctuations (RMSF) were calculated for all Cα atoms of all XynA domain residues (residue 1–185) over the final 100 ns. c Three-dimensional structure of the XynA highlighting the catalytic cavity located between the palm and fingers domains. Access to the active site cleft is determined by the orientation of the thumb domain. The structure representations were prepared using the PyMol software [82].