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A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps.
- Source :
- Acta Crystallographica: Section D (Wiley-Blackwell); Jul2001, Vol. 57 Issue 7, p1013-1019, 7p
- Publication Year :
- 2001
-
Abstract
- The classical approach to building the amino-acid residues into the initial electron-density map requires days to weeks of a skilled investigator's time. Automating this procedure should not only save time, but has the potential to provide a more accurate starting model for input to refinement programs. The new software routine MAID builds the protein structure into the electron-density map in a series of sequential steps. The first step is the fitting of the secondary α-helix and, β-sheet structures. These `fits' are then used to determine the local amino-acid sequence assignment. These assigned fits are then extended through the loop regions and fused with the neighboring sheet or helix. The program was tested on the unaveraged 2.5 Å selenomethionine multiple-wavelength anomalous dispersion (SMAD) electron-density map that was originally used to solve the structure of the 291-residue protein human heart short-chain L-3-hydroxyacyl-COA dehydrogenase (SHAD). Inputting just the map density and the amino-acid sequence, MAID fitted 80% of the residues with an r.m.s.d. error of 0.43 Å for the main-chain atoms and 1.0 Å for all atoms without any user intervention. When tested on a higher quality 1.9 Å SMAD map, MAID correctly fitted 100% (418) of the residues. A major advantage of the MAID fitting procedure is that it maintains ideal bond lengths and angles and constrains ψ/&psi angles to the appropriate Ramachandran regions. Recycling the output of this new routine through a partial structure-refinement program may have the potential to completely automate the fitting of electron-density maps. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 09074449
- Volume :
- 57
- Issue :
- 7
- Database :
- Complementary Index
- Journal :
- Acta Crystallographica: Section D (Wiley-Blackwell)
- Publication Type :
- Academic Journal
- Accession number :
- 15000741
- Full Text :
- https://doi.org/10.1107/S0907444901006394