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Erkang Fan,
David Baker,
Stanley Fields,
Michael H Gelb,
Frederick S Buckner,
Wesley C Van Voorhis,
Eric Phizicky,
Mark Dumont,
Christopher Mehlin,
Elizabeth Grayhack, [......],
Joseph Luft,
Larry Desoto,
Mark Holl,
Jonathan Caruthers,
Jürgen Bosch,
Mark Robien, Tracy Arakaki,
Margaret Holmes,
Isolde Le Trong,
Wim G J Hol
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ABSTRACT: The Structural Genomics of Pathogenic Protozoa (SGPP) Consortium aimed to determine crystal structures of proteins from trypanosomatid and malaria parasites in a high throughput manner. The pipeline of target selection, protein production, crystallization, and structure determination, is sketched. Special emphasis is given to a number of technology developments including domain prediction, the use of "co-crystallants," and capillary crystallization. "Fragment cocktail crystallography" for medical structural genomics is also described.
Methods in molecular biology (Clifton, N.J.) 02/2008; 426:497-513.
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Tracy Arakaki,
Helen Neely,
Erica Boni,
Natasha Mueller,
Frederick S Buckner,
Wesley C Van Voorhis,
Angela Lauricella,
George DeTitta,
Joseph Luft,
Wim G J Hol,
Ethan A Merritt
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ABSTRACT: The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 A using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed alpha-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 04/2007; 63(Pt 3):178-82. · 0.51 Impact Factor
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Tracy Arakaki,
Isolde Le Trong,
Eric Phizicky,
Erin Quartley,
George DeTitta,
Joseph Luft,
Angela Lauricella,
Lori Anderson,
Oleksandr Kalyuzhniy,
Elizabeth Worthey,
Peter J Myler,
David Kim,
David Baker,
Wim G J Hol,
Ethan A Merritt
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ABSTRACT: The gene product of structural genomics target Lmaj006129 from Leishmania major codes for a 164-residue protein of unknown function. When SeMet expression of the full-length gene product failed, several truncation variants were created with the aid of Ginzu, a domain-prediction method. 11 truncations were selected for expression, purification and crystallization based upon secondary-structure elements and disorder. The structure of one of these variants, Lmaj006129AAH, was solved by multiple-wavelength anomalous diffraction (MAD) using ELVES, an automatic protein crystal structure-determination system. This model was then successfully used as a molecular-replacement probe for the parent full-length target, Lmaj006129AAA. The final structure of Lmaj006129AAA was refined to an R value of 0.185 (Rfree = 0.229) at 1.60 A resolution. Structure and sequence comparisons based on Lmaj006129AAA suggest that proteins belonging to Pfam sequence families PF04543 and PF01878 may share a common ligand-binding motif.
Acta Crystallographica Section F Structural Biology and Crystallization Communications 04/2006; 62(Pt 3):175-9. · 0.51 Impact Factor
