4TNN
Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.
Summary for 4TNN
| Entry DOI | 10.2210/pdb4tnn/pdb |
| Descriptor | Metal-binding lipocalin, SULFATE ION, NICKEL (II) ION, ... (4 entities in total) |
| Functional Keywords | yoda, purification artifact, metal-binding lipocalin, metal binding protein |
| Biological source | Escherichia coli str. K-12 substr. MC4100 |
| Total number of polymer chains | 1 |
| Total formula weight | 23008.95 |
| Authors | Gasiorowska, O.A.,Cymborowski, M.T.,Handing, K.B.,Shabalin, I.G.,Zasadzinska, E.,Niedzialkowska, E.,Porebski, P.J.,Minor, W. (deposition date: 2014-06-04, release date: 2014-06-25, Last modification date: 2024-10-30) |
| Primary citation | Niedzialkowska, E.,Gasiorowska, O.,Handing, K.B.,Majorek, K.A.,Porebski, P.J.,Shabalin, I.G.,Zasadzinska, E.,Cymborowski, M.,Minor, W. Protein purification and crystallization artifacts: The tale usually not told. Protein Sci., 25:720-733, 2016 Cited by PubMed Abstract: 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. PubMed: 26660914DOI: 10.1002/pro.2861 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.951 Å) |
Structure validation
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