1VIV

Crystal structure of a hypothetical protein

Summary for 1VIV

• Entry DOI: 10.2210/pdb1viv/pdb
• Descriptor: Hypothetical protein yckF (2 entities in total)
• Functional Keywords: structural genomics, unknown function
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 42690.62

Authors

Structural GenomiX (deposition date: 2003-12-01, release date: 2003-12-30, Last modification date: 2023-12-27)

Primary citation

Badger, J.,Sauder, J.M.,Adams, J.M.,Antonysamy, S.,Bain, K.,Bergseid, M.G.,Buchanan, S.G.,Buchanan, M.D.,Batiyenko, Y.,Christopher, J.A.,Emtage, S.,Eroshkina, A.,Feil, I.,Furlong, E.B.,Gajiwala, K.S.,Gao, X.,He, D.,Hendle, J.,Huber, A.,Hoda, K.,Kearins, P.,Kissinger, C.,Laubert, B.,Lewis, H.A.,Lin, J.,Loomis, K.,Lorimer, D.,Louie, G.,Maletic, M.,Marsh, C.D.,Miller, I.,Molinari, J.,Muller-Dieckmann, H.J.,Newman, J.M.,Noland, B.W.,Pagarigan, B.,Park, F.,Peat, T.S.,Post, K.W.,Radojicic, S.,Ramos, A.,Romero, R.,Rutter, M.E.,Sanderson, W.E.,Schwinn, K.D.,Tresser, J.,Winhoven, J.,Wright, T.A.,Wu, L.,Xu, J.,Harris, T.J.
Structural analysis of a set of proteins resulting from a bacterial genomics project
Proteins, 60:787-796, 2005

PubMed Abstract: The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

PubMed: 16021622
DOI: 10.1002/prot.20541

Experimental method

X-RAY DIFFRACTION (2.6 Å)