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| | <StructureSection load='4tnn' size='340' side='right'caption='[[4tnn]], [[Resolution|resolution]] 1.95Å' scene=''> | | <StructureSection load='4tnn' size='340' side='right'caption='[[4tnn]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4tnn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mc4100 Escherichia coli str. k-12 substr. mc4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4tnn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MC4100 Escherichia coli str. K-12 substr. MC4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TNN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.951Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yodA, BN896_1774 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1403831 Escherichia coli str. K-12 substr. MC4100])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnn OCA], [http://pdbe.org/4tnn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tnn RCSB], [http://www.ebi.ac.uk/pdbsum/4tnn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnn ProSAT]</span></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=4tnn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnn OCA], [https://pdbe.org/4tnn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tnn RCSB], [https://www.ebi.ac.uk/pdbsum/4tnn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnn ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli str. k-12 substr. mc4100]] | + | [[Category: Escherichia coli str. K-12 substr. MC4100]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cymborowski, M T]] | + | [[Category: Cymborowski MT]] |
| - | [[Category: Gasiorowska, O A]] | + | [[Category: Gasiorowska OA]] |
| - | [[Category: Handing, K B]] | + | [[Category: Handing KB]] |
| - | [[Category: Minor, W]] | + | [[Category: Minor W]] |
| - | [[Category: Niedzialkowska, E]] | + | [[Category: Niedzialkowska E]] |
| - | [[Category: Porebski, P J]] | + | [[Category: Porebski PJ]] |
| - | [[Category: Shabalin, I G]] | + | [[Category: Shabalin IG]] |
| - | [[Category: Zasadzinska, E]] | + | [[Category: Zasadzinska E]] |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Metal-binding lipocalin]]
| + | |
| - | [[Category: Purification artifact]]
| + | |
| - | [[Category: Yoda]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building.
Protein purification and crystallization artifacts: The tale usually not told.,Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W Protein Sci. 2016 Mar;25(3):720-33. doi: 10.1002/pro.2861. Epub 2016 Jan 26. PMID:26660914[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W. Protein purification and crystallization artifacts: The tale usually not told. Protein Sci. 2016 Mar;25(3):720-33. doi: 10.1002/pro.2861. Epub 2016 Jan 26. PMID:26660914 doi:http://dx.doi.org/10.1002/pro.2861
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