Crystal packing of Bmlp3-p21 and Bmlp3-c2.

<p>Four protein molecules (shades of blue) are present in the asymmetric unit of Bmlp3-p21 (A), whereas the asymmetric unit of Bmlp3-c2 (B) contains a dimeric assembly (red and pink). Symmetry-related molecules are shown in gray.</p

Biophysical parameters for the Bmlp3 and Bmlp7 proteins calculated using ProtParam (http://web.expasy.org/protparam/).

<p>Biophysical parameters for the Bmlp3 and Bmlp7 proteins calculated using ProtParam (<a href="http://web.expasy.org/protparam/" target="_blank">http://web.expasy.org/protparam/</a>).</p

Electron density maps of Bmlp3-p21.

<p>Bmlp3-p21 is the first structure of a member of the 30-kDa lipoprotein family with complete sequence included in the model. All amino acids from the N-terminus (A) to the C-terminus were clearly identified in the electron density maps. Moreover, the quality of the electron density maps allowed for the definite identification of the protein. In most cases, the electron density of the side chains was very clear, as illustrated for Tyr116 (B) and Leu131 (C). The 2Fo-Fc maps are displayed in blue at the 1.0σ level.</p

Structural comparison of Bmlp3-p21, Bmlp3-c2 and Bmlp7.

<p>The structures of Bmlp3-p21 (chain A), Bmlp3-c2 (chains A and B) and Bmlp7 (chain A) were Cα-superposed using COOT <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061303#pone.0061303-Emsley1" target="_blank">[28]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061303#pone.0061303-Emsley2" target="_blank">[29]</a>. The main deviations are found in the CTD domain, in loop conformation. The most flexible loop and the N-terminus are encircled.</p

Electrostatic surface potential of Bmlp3 calculated at pH 7.4.

<p>Two different views of the surface potential of Bmlp3 are shown. The positive and negative charges are colored blue and red, respectively. The loop containing the putative cell-penetrating signal sequence is marked with a circle.</p

Potential binding sites of the Bmlp3 protein.

a<p>The volume of cavity No. 4 was estimated to be 60 ų, however, it might be larger than predicted upon even a slight movement of the helices in the NTD.</p

Potential Bmlp3 binding sites.

<p>Molecular cavities as putative binding sites of Bmlp3 (A) are marked by No. 1–4, as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061303#pone-0061303-t003" target="_blank">Table 3</a>. Cavity No. 4 (view at the top of the protein molecule, B) is the only pocket formed entirely in the NTD. Cavity No. 1 (C) has an elongated shape and might be a binding site for docking of a fatty acid chain, as well as of an oligosaccharide. A fragment of a PEG molecule from the crystallization solution is bound in cavity No. 1 of chains A and D of Bmlp3-p21 (D).</p

The iodide ion binding site in Bmlp3-c2.

<p>An iodide anion from the crystallization solution is present between chains A (orange) and B (magenta) of Bmlp3-c2. The N…I and O…I distances are in Å. The anomalous (A) and the 2Fo-Fc (B) maps are displayed at the iodide site at 5.0σ and at 1.0σ, respectively.</p