(A) Stereo ribbon diagram of PA3611 color-coded from N-terminus (blue) to C-terminus (red). Helices H1-H5, β-strands (B1-B5) and the Cys92-Cys130 disulfide bond are indicated. (B) Diagram showing the secondary structure elements of PA3611 superimposed on its primary sequence, adapted from PDBSum (http://www.ebi.ac.uk/pdbsum). The α-helices (H1-H5), β-strands (B1-B5), β-turns (β) and β-hairpins (red loops) are indicated. The sequence and structure includes Gly0, which remains after removal of the expression and purification tag, and residues 20–131 of the 136 residues in the entire protein.

Residue conservation analysis performed using CONSURF of PA3611(UniProt Q9HY15) homologs included in the analysis (with UniProt id codes and sequence identities to PA3611 in parentheses): PSPPH_3802 from Pseudomonas syringae pv. phaseolicola str. 1448A (Q48F97, 70%), PPUT_4084 from Pseudomonas putida str F1 (A5W7U8, 57%), PFL01_1180 from Pseudomonas fluorescens str Pf0-1 (Q3KH33, 59%), PFLU_1192 from Pseudomonas fluorescens str SBW25 (C3KDG3, 52%). The surface representation color gradient goes from cyan (most variable) to magenta (most conserved). Most of the conserved residues in PA3611 and its homologs are located on one side of the protein and are located on the surface or surround a prominent groove in the protein. They include Ser38, Arg44, Ile46, Tyr55, Val 83, Gln86, Ser90, Asn94, Arg98 and Tyr109 (labeled in left panel; orientation is similar to that in ). Right panel: ~180° rotation around a vertical axis compared to the left panel.

PA3611 (blue) is structurally similar to the C-terminal RNA-binding domain of E. coli Era GTPase (grey). Some of the Era residues (red sticks) implicated in RNA binding (Arg239, Lys244, Lys255 and Lys263) approximate the location of PA3611 residues (blue sticks) Arg69, Arg75, Arg77, Arg84 and Arg98, respectively. Although, only Arg98 is conserved in PA3611 homologs, the similar chemical nature of the residues leads to a similar basic region on both proteins. PA3611 Arg131, which is not a counterpart of any Era residues, also contributes to the basic nature of this region and might be involved in ligand or nucleic acid interactions.

Superimposition of PA3611 (in blue to red from N- to C-terminus, similar orientation as in ) with the E. coli Era GTPase (grey) using DaliLite (Z-score=3.2, r.m.s.d of 3.2 Å over 71 Cα residues) highlighting the significant structural differences in helix positions but the FATCAT flexible alignment mode is still able to identify the overall structural similarity between PA3611 and the C-terminal RNA-binding domain of Era.

The electrostatic surface representation of PA3611 shows an almost equal distribution of positively- and negatively-charged residues (blue and red, respectively) on the protein surface. The basic region (blue) is primarily made up of residues described in . The molecular orientation is similar to that in . The color scale is in units of kT/e from −3 to +3.