2m5x: Difference between revisions
New page: '''Unreleased structure''' The entry 2m5x is ON HOLD Authors: Lenarcic Zivkovic, M., Dvornyk, A., Kludkiewicz, B., Kopera, E., Zagorski-Ostoja, W., Grzelak, K., Zhukov, I., Bal, W. Des... |
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==Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.== | |||
<StructureSection load='2m5x' size='340' side='right'caption='[[2m5x]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2m5x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Galleria_mellonella Galleria mellonella]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M5X FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 17 models</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m5x OCA], [https://pdbe.org/2m5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m5x RCSB], [https://www.ebi.ac.uk/pdbsum/2m5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m5x ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q968S7_GALME Q968S7_GALME] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 A 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 beta2alphabeta fold characteristic for Kazal-family serine proteinase inhibitors. | |||
Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor.,Kopera E, Bal W, Lenarcic Zivkovic M, Dvornyk A, Kludkiewicz B, Grzelak K, Zhukov I, Zagorski-Ostoja W, Jaskolski M, Krzywda S PLoS One. 2014 Sep 18;9(9):e106936. doi: 10.1371/journal.pone.0106936., eCollection 2014. PMID:25233114<ref>PMID:25233114</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2m5x" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Galleria mellonella]] | |||
[[Category: Large Structures]] | |||
[[Category: Bal W]] | |||
[[Category: Dvornyk A]] | |||
[[Category: Grzelak K]] | |||
[[Category: Kludkiewicz B]] | |||
[[Category: Kopera E]] | |||
[[Category: Lenarcic Zivkovic M]] | |||
[[Category: Zagorski-Ostoja W]] | |||
[[Category: Zhukov I]] | |||
Latest revision as of 11:18, 30 October 2024
Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.
Structural highlights
FunctionPublication Abstract from PubMedPurification 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 A 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 beta2alphabeta fold characteristic for Kazal-family serine proteinase inhibitors. Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor.,Kopera E, Bal W, Lenarcic Zivkovic M, Dvornyk A, Kludkiewicz B, Grzelak K, Zhukov I, Zagorski-Ostoja W, Jaskolski M, Krzywda S PLoS One. 2014 Sep 18;9(9):e106936. doi: 10.1371/journal.pone.0106936., eCollection 2014. PMID:25233114[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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