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The befores and afters of molecular replacement.

Dodson E - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements.Once a solution has been found it must be refined, which can be challenging for low-homology models.There is a detailed discussion of structures used as examples for CCP4 tutorials.

View Article: PubMed Central - HTML - PubMed

Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, England. e.dodson@ysbl.york.ac.uk

ABSTRACT
This review addresses the essential questions to consider when attempting to phase a new crystal structure using molecular replacement. Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements. Once a solution has been found it must be refined, which can be challenging for low-homology models. There is a detailed discussion of structures used as examples for CCP4 tutorials.

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Matching the S100 sequence against the EBI databases. (a) Some of the matching sequences found by the MSDtarget pairwise alignment. Those with associated three-dimensional models are shown in green. (b) The pairwise alignment for one of the models, 1irj. (c) The overlap, based on one chain only, of the final S100 dimer model, 1e8a, onto the 1irj dimer. The two chains of the S100 dimer are shown in green and blue and those of the 1irj dimer in yellow and tan. Clearly, the second chains do not match well. (d) The overlap of 1e8a onto the 1mho dimer using the same colour scheme. Although the matched chains do not fit so well, the relative orientation of the monomers is closer than that for 1irj.
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fig1: Matching the S100 sequence against the EBI databases. (a) Some of the matching sequences found by the MSDtarget pairwise alignment. Those with associated three-dimensional models are shown in green. (b) The pairwise alignment for one of the models, 1irj. (c) The overlap, based on one chain only, of the final S100 dimer model, 1e8a, onto the 1irj dimer. The two chains of the S100 dimer are shown in green and blue and those of the 1irj dimer in yellow and tan. Clearly, the second chains do not match well. (d) The overlap of 1e8a onto the 1mho dimer using the same colour scheme. Although the matched chains do not fit so well, the relative orientation of the monomers is closer than that for 1irj.

Mentions: This structure has been deposited with PDB code 1e8a (Moroz et al., 2001 ▶). Some of the MSDtarget output obtained from the S100 sequence search is given in Fig. 1 ▶(a); Fig. 1 ▶(b) shows the pairwise matches. I will discuss models 1irj (41% sequence identity) and 1mho (39% sequence identity).


The befores and afters of molecular replacement.

Dodson E - Acta Crystallogr. D Biol. Crystallogr. (2007)

Matching the S100 sequence against the EBI databases. (a) Some of the matching sequences found by the MSDtarget pairwise alignment. Those with associated three-dimensional models are shown in green. (b) The pairwise alignment for one of the models, 1irj. (c) The overlap, based on one chain only, of the final S100 dimer model, 1e8a, onto the 1irj dimer. The two chains of the S100 dimer are shown in green and blue and those of the 1irj dimer in yellow and tan. Clearly, the second chains do not match well. (d) The overlap of 1e8a onto the 1mho dimer using the same colour scheme. Although the matched chains do not fit so well, the relative orientation of the monomers is closer than that for 1irj.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394785&req=5

fig1: Matching the S100 sequence against the EBI databases. (a) Some of the matching sequences found by the MSDtarget pairwise alignment. Those with associated three-dimensional models are shown in green. (b) The pairwise alignment for one of the models, 1irj. (c) The overlap, based on one chain only, of the final S100 dimer model, 1e8a, onto the 1irj dimer. The two chains of the S100 dimer are shown in green and blue and those of the 1irj dimer in yellow and tan. Clearly, the second chains do not match well. (d) The overlap of 1e8a onto the 1mho dimer using the same colour scheme. Although the matched chains do not fit so well, the relative orientation of the monomers is closer than that for 1irj.
Mentions: This structure has been deposited with PDB code 1e8a (Moroz et al., 2001 ▶). Some of the MSDtarget output obtained from the S100 sequence search is given in Fig. 1 ▶(a); Fig. 1 ▶(b) shows the pairwise matches. I will discuss models 1irj (41% sequence identity) and 1mho (39% sequence identity).

Bottom Line: Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements.Once a solution has been found it must be refined, which can be challenging for low-homology models.There is a detailed discussion of structures used as examples for CCP4 tutorials.

View Article: PubMed Central - HTML - PubMed

Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, England. e.dodson@ysbl.york.ac.uk

ABSTRACT
This review addresses the essential questions to consider when attempting to phase a new crystal structure using molecular replacement. Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements. Once a solution has been found it must be refined, which can be challenging for low-homology models. There is a detailed discussion of structures used as examples for CCP4 tutorials.

Show MeSH