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Crystallographic refinement of ligand complexes.

Kleywegt GJ - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities.Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities.A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

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Affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden.

ABSTRACT
Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

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Electron density for the inhibitor BABIM (shown with gold C atoms) in its complex with botulinum neurotoxin type B protease (Hanson et al., 2000 ▶, 2002 ▶). The map is a 2mF                  o − DF                  c synthesis, calculated with all deposited data (2.5 Å), and taken from EDS (Kleywegt et al., 2004 ▶). Figs. 2 and 3 were created with O (Jones et al., 1991 ▶) and MolRay (Harris & Jones, 2001 ▶).
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fig2: Electron density for the inhibitor BABIM (shown with gold C atoms) in its complex with botulinum neurotoxin type B protease (Hanson et al., 2000 ▶, 2002 ▶). The map is a 2mF o − DF c synthesis, calculated with all deposited data (2.5 Å), and taken from EDS (Kleywegt et al., 2004 ▶). Figs. 2 and 3 were created with O (Jones et al., 1991 ▶) and MolRay (Harris & Jones, 2001 ▶).

Mentions: Sometimes a ligand simply does not bind (or binds with too low occupancy or with too much disorder) and this may explain what happened in the structure determination of a complex between botulinum neurotoxin type B protease and an inhibitor (Hanson et al., 2000 ▶). Close inspection of the maps after publication convinced the authors that these did ‘not support the placement of the inhibitor as stated in the paper’ and the structure was retracted (Hanson et al., 2002 ▶; Fig. 2 ▶).


Crystallographic refinement of ligand complexes.

Kleywegt GJ - Acta Crystallogr. D Biol. Crystallogr. (2006)

Electron density for the inhibitor BABIM (shown with gold C atoms) in its complex with botulinum neurotoxin type B protease (Hanson et al., 2000 ▶, 2002 ▶). The map is a 2mF                  o − DF                  c synthesis, calculated with all deposited data (2.5 Å), and taken from EDS (Kleywegt et al., 2004 ▶). Figs. 2 and 3 were created with O (Jones et al., 1991 ▶) and MolRay (Harris & Jones, 2001 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483469&req=5

fig2: Electron density for the inhibitor BABIM (shown with gold C atoms) in its complex with botulinum neurotoxin type B protease (Hanson et al., 2000 ▶, 2002 ▶). The map is a 2mF o − DF c synthesis, calculated with all deposited data (2.5 Å), and taken from EDS (Kleywegt et al., 2004 ▶). Figs. 2 and 3 were created with O (Jones et al., 1991 ▶) and MolRay (Harris & Jones, 2001 ▶).
Mentions: Sometimes a ligand simply does not bind (or binds with too low occupancy or with too much disorder) and this may explain what happened in the structure determination of a complex between botulinum neurotoxin type B protease and an inhibitor (Hanson et al., 2000 ▶). Close inspection of the maps after publication convinced the authors that these did ‘not support the placement of the inhibitor as stated in the paper’ and the structure was retracted (Hanson et al., 2002 ▶; Fig. 2 ▶).

Bottom Line: Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities.Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities.A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden.

ABSTRACT
Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.

Show MeSH