Evidence for alternative quaternary structure in a bacterial Type III secretion system chaperone

BMC Structural Biology

Table 2 Superposition Analysis for Selected Monomers and Dimers as Determined by Local-Global Alignment

Structure 1	Structure 2	Corresponding Cα positions^a	RMSD (Å)	Sequence Identity (%)	LGA_S^c
IpgC^1-151 (chain A)	IpgC^10-155	122/137	0.80	99.18^b	88.32
IpgC^1-151 (chain B)	IpgC^10-155	123/137	1.01	100.00	87.62
SycD^21-163 (chain A)	IpgC^10-155	120/137	1.56	25.83	80.61
SycD^21-163 (AU)	IpgC^10-155 (chains A&B)	199/274	2.34	18.59	51.27
IpgC^1-151 (AU)	IpgC^10-155 (chains A&B)	135/274	1.35	93.33	48.14

^aDenotes the number of residues from structure 1 that superimpose within 4.0 Å distance of an equivalent position in structure 2.
^bEven though the actual sequence identity between these two samples is 100%, the Cα location of A30 in chain of A of the IpgC^1-151 structure actually lies closer to that of I28 of IpgC^10-155 when these two structures are superimposed.
^cThe LGA_S parameter represents a scoring function to evaluate the overall levels of structural similarity between two sets of coordinates. For each set of corresponding residues, it combines information pertaining to both the faction of residues that overlap within a given RMSD window as well as those that overlap within a given distance cutoff[10].

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