Unusual sequence numbering: Difference between revisions
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===Missing Residues=== | ===Missing Residues=== | ||
[[Image:Sequence-missing-loop-2ace.png|frame|Excerpt from PDB file 2ace showing gap in sequence numbering due to a missing loop.]] | [[Image:Sequence-missing-loop-2ace.png|frame|Excerpt from PDB file 2ace showing gap in sequence numbering due to a missing loop.]] | ||
It is not uncommon for a surface loop of the crystallized protein to be disordered. Often such loops are [[Intrinsically Disordered Protein|intrinsically disordered]]. The disorder blurs the electron density map for that loop, and the loop residues are not given coordinates in the model: they are missing in the model. However, they were not missing in the crystallized protein. This causes a gap in the sequence numbers in the PDB file. An example is [http://firstglance.jmol.org/fg.htm?mol=2ace 2ace] ([[2ace]]). Residues 485-489 are missing in the 3D crystallographic model due to disorder in the crystal. Also missing are 3 N-terminal, and 2 C-terminal residues. FirstGlance in Jmol tabulates missing residues, and marks regions of the 3D model where residues are missing with "empty baskets". | It is not uncommon for a surface loop of the crystallized protein to be disordered. Often such loops are [[Intrinsically Disordered Protein|intrinsically disordered]]. The disorder blurs the electron density map for that loop, and the loop residues are not given coordinates in the model: they are [[Missing residues and incomplete sidechains|missing in the model]]. However, they were not missing in the crystallized protein. This causes a gap in the sequence numbers in the PDB file. An example is [http://firstglance.jmol.org/fg.htm?mol=2ace 2ace] ([[2ace]]). Residues 485-489 are missing in the 3D crystallographic model due to disorder in the crystal. Also missing are 3 N-terminal, and 2 C-terminal residues. FirstGlance in Jmol tabulates missing residues, and marks regions of the 3D model where residues are missing with "empty baskets". | ||
:<table width=550><tr><td>[[Image:2ace-empty-basket.png|center]]</td><td>"Empty Basket": Closeup of the region of [[2ace]] where residues 485-489 are missing. In [[FirstGlance in Jmol]], empty baskets alert the user to missing residues. ("S-" labels residues with missing sidechain atoms.)</td></tr></table> | :<table width=550><tr><td>[[Image:2ace-empty-basket.png|center]]</td><td>"Empty Basket": Closeup of the region of [[2ace]] where residues 485-489 are missing. In [[FirstGlance in Jmol]], empty baskets alert the user to missing residues. ("S-" labels residues with missing sidechain atoms.)</td></tr></table> | ||