6OBY

The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.

Summary for 6OBY

• Entry DOI: 10.2210/pdb6oby/pdb
• Descriptor: Iron-sulfur cluster carrier protein, ADENOSINE-5'-DIPHOSPHATE, COBALT (II) ION, ... (4 entities in total)
• Functional Keywords: alpha-beta protein, pixe, metal transport
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 2
• Total formula weight: 59839.28

Authors

Snell, E.H.,Garman, E.F.,Lowe, E.D. (deposition date: 2019-03-21, release date: 2019-12-25, Last modification date: 2020-01-22)

Primary citation

Grime, G.W.,Zeldin, O.B.,Snell, M.E.,Lowe, E.D.,Hunt, J.F.,Montelione, G.T.,Tong, L.,Snell, E.H.,Garman, E.F.
High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.
J.Am.Chem.Soc., 142:185-197, 2020

PubMed Abstract: Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ion beam analysis through particle induced X-ray emission (PIXE), we have quantitatively identified the metal atoms in 30 previously structurally characterized proteins using minimal sample volume and a high-throughput approach. Over half of these metals had been misidentified in the deposited structural models. Some of the PIXE detected metals not seen in the models were explainable as artifacts from promiscuous crystallization reagents. For others, using the correct metal improved the structural models. For multinuclear sites, anomalous diffraction signals enabled the positioning of the correct metals to reveal previously obscured biological information. PIXE is insensitive to the chemical environment, but coupled with experimental diffraction data deposited alongside the structural model it enables validation and potential remediation of metalloprotein models, improving structural and, more importantly, mechanistic knowledge.

PubMed: 31794207
DOI: 10.1021/jacs.9b09186

Experimental method

X-RAY DIFFRACTION (2.87 Å)