Computational protocol: Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein

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Protocol publication

[…] IBPv shares low sequence identity (29%) with the ice binding protein LeIBP from Arctic yeast Leucosporidium sp. for which crystal structure is known []. According to the sequence alignment, there are two copies of LeIBP per one molecule of IBPv. The molecular replacement procedure was applied to locate a solution using the program MOLREP []. A monomer of LeIBP (PDB accession code 3UYU) was used as a search model. A total of four LeIBP monomers were located in the asymmetric unit of IBP.The positioned MR model was refined using the maximum likelihood refinement in REFMAC [] with the TLS parameters generated by the TLSMD server []. TLS tensors were analyzed, and anisotropic B-factors were derived with TLSANL program []. The program Coot was used for model building throughout the refinement []. The final model consists of protein residues 23–445 for protein molecule A, 23–446 for protein molecule B, one nitrate anion and 684 water molecules. Alternate conformations have been built for protein residues T127, R221, I247, V345, I413 (molecule A) and T127, T179, K184, R221 (molecule B). 98% of residues lie in the favored region of the Ramachandran plot with no residues in the disallowed region. The atomic coordinates and structure factors (code 5UYT) have been deposited in the Protein Data Bank. [...] The structural alignment of IBPv_a, IBPv_b and their homologous proteins, namely LeIBP (PDB: 3UYU) [], TisAFP6 (PDB: 3VN3) [], TisAFP8 (PDB: 5B5H) [], FfIBP (PDB: 4NU2) [] and ColAFP (PDB: 3WP9) [], was performed using Multiseq under VMD platform []. The structures were colored by structural similarities (Qres) or sequence similarities (BLOSUM 60). All the structure figures were generated using Pymol []. […]

Pipeline specifications

Software tools Molrep, Coot, VMD, PyMOL
Application Protein structure analysis