4HGU
Crystal Structure of Galleria mellonella Silk Protease Inhibitor 2
Summary for 4HGU
| Entry DOI | 10.2210/pdb4hgu/pdb |
| Related | 1AN1 2OVO 3PIS |
| Descriptor | Silk protease inhibitor 2, SODIUM ION (3 entities in total) |
| Functional Keywords | kazal-type serine protease inhibitor, hydrolase inhibitor |
| Biological source | Galleria mellonella (Greater wax moth) |
| Total number of polymer chains | 1 |
| Total formula weight | 4409.70 |
| Authors | Krzywda, S.,Jaskolski, M.,Dvornyk, A.,Kludkiewicz, B.,Grzelak, K.,Zagorski, W.,Bal, W.,Kopera, E. (deposition date: 2012-10-08, release date: 2013-10-09, Last modification date: 2024-10-30) |
| Primary citation | Kopera, E.,Bal, W.,Lenarcic Zivkovic, M.,Dvornyk, A.,Kludkiewicz, B.,Grzelak, K.,Zhukov, I.,Zagorski-Ostoja, W.,Jaskolski, M.,Krzywda, S. Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor. Plos One, 9:e106936-e106936, 2014 Cited by PubMed Abstract: Purification of suitable quantity of homogenous protein is very often the bottleneck in protein structural studies. Overexpression of a desired gene and attachment of enzymatically cleavable affinity tags to the protein of interest made a breakthrough in this field. Here we describe the structure of Galleria mellonella silk proteinase inhibitor 2 (GmSPI-2) determined both by X-ray diffraction and NMR spectroscopy methods. GmSPI-2 was purified using a new method consisting in non-enzymatic His-tag removal based on a highly specific peptide bond cleavage reaction assisted by Ni(II) ions. The X-ray crystal structure of GmSPI-2 was refined against diffraction data extending to 0.98 Å resolution measured at 100 K using synchrotron radiation. Anisotropic refinement with the removal of stereochemical restraints for the well-ordered parts of the structure converged with R factor of 10.57% and Rfree of 12.91%. The 3D structure of GmSPI-2 protein in solution was solved on the basis of 503 distance constraints, 10 hydrogen bonds and 26 torsion angle restraints. It exhibits good geometry and side-chain packing parameters. The models of the protein structure obtained by X-ray diffraction and NMR spectroscopy are very similar to each other and reveal the same β2αβ fold characteristic for Kazal-family serine proteinase inhibitors. PubMed: 25233114DOI: 10.1371/journal.pone.0106936 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (0.98 Å) |
Structure validation
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