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PcaA

PcaA. Mycolic acid cyclopropyl synthase (Smith&Sacchettini) original structure solved at 2.0A via MAD R-value = 0.22, R-free = 0.27 287 residues, a/b fold. Example of density quality (~1 s contour with C a trace). Electron density map (2.8A). Results of tracing.

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PcaA

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  1. PcaA • Mycolic acid cyclopropyl synthase (Smith&Sacchettini) • original structure solved at 2.0A via MAD R-value = 0.22, R-free = 0.27 • 287 residues, a/b fold Example of density quality (~1s contour with Ca trace)

  2. Electron density map (2.8A)

  3. Results of tracing

  4. Strip off branches of trace (linearize)

  5. Linearized trace shows backbone connectivity

  6. Pick Ca’s using neural net; link together

  7. Results of CAPRA

  8. Comparison to backbone of true structure (white) Percent built = 89% (missing: 15-residue N-terminus, 17-residue disordered loop) 4 single-atom insertions; 5 single-atom deletions RMSD = 0.81A

  9. CAPRA model consists of 3 chains Chain lengths: 14, 96, 145 residues

  10. Results of LOOKUP (modeling side-chains)

  11. Comparison of TEXTAL model to true structure Percent amino acid identity = 87.5% (mistakes: small frame-shifts around gaps in alignment) all-atom RMSD = 0.92A

  12. Closeup of b-strand (TEXTAL model in green)

  13. Closeup of a-helix (TEXTAL model in green)

  14. If5A • Translation initiation factor 5A (Peat&Terwilliger) • 136 residues, b-fold • original structure solved at 1.75A by MAD R-value = 0.21, R-free = 0.24 Example of density quality (~1s contour with Ca trace)

  15. Electron density map (2.8A) with Ca chains generated by CAPRA (CAPRA chains shown in color; true backbone shown in white)

  16. Results of CAPRA Percent built = 94% chain lengths: 16, 20, 44, 57 Ca RMSD = 0.76A

  17. LOOKUP: fitting side-chains into density

  18. Results of LOOKUP, comparison to true structure Percent identity = 84% all-atom RMSD = 0.92A (TEXTAL model in green; true structure in red/white/blue)

  19. Focus on backbone atoms Notice accuracy of carbonyl oxygens and chain directionality

  20. Closeup of a strand within a b-sheet

  21. Closeup of another b-strand and turn

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