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NCS-constrained exhaustive search using oligomeric models.

Isupov MN, Lebedev AA - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted.In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search.Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.

View Article: PubMed Central - HTML - PubMed

Affiliation: Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England. m.isupov@exeter.ac.uk

ABSTRACT
The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.

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Solution of the structure of anti-TRAP from B. licheniformis. (a) Ribbon diagram of the dodecamer of anti-TRAP from B. subtilis. (b) Native Patterson synthesis, in which three strong non-equivalent non-origin peaks are present. (c) 120° and 180° sections of an SRF, indicating the orientations of twofold and threefold NCS axes. The trimeric search model (centre) was oriented so that its threefold molecular axis was aligned with the NCS threefold axis (red lines). TF searches were performed for a series of orientations related to that shown by a rotation around the molecular threefold axis by the variable angle χ. (d) The highest CC in the TF search is plotted as a function of χ. (e) The MR solution with four dodecamers in the asymmetric unit, which are related by the translational NCS. This figure was prepared using BOBSCRIPT, MOLREP, CCP4mg (Potterton et al., 2004 ▶) and R.
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fig3: Solution of the structure of anti-TRAP from B. licheniformis. (a) Ribbon diagram of the dodecamer of anti-TRAP from B. subtilis. (b) Native Patterson synthesis, in which three strong non-equivalent non-origin peaks are present. (c) 120° and 180° sections of an SRF, indicating the orientations of twofold and threefold NCS axes. The trimeric search model (centre) was oriented so that its threefold molecular axis was aligned with the NCS threefold axis (red lines). TF searches were performed for a series of orientations related to that shown by a rotation around the molecular threefold axis by the variable angle χ. (d) The highest CC in the TF search is plotted as a function of χ. (e) The MR solution with four dodecamers in the asymmetric unit, which are related by the translational NCS. This figure was prepared using BOBSCRIPT, MOLREP, CCP4mg (Potterton et al., 2004 ▶) and R.

Mentions: Anti-TRAP is a small protein of 53 amino acids which regulates the activity of tryptophan attenuation protein (TRAP; Antson et al., 1999 ▶) in Bacillus. Anti-TRAP from B. licheniformis was crystallized in space group P21, with unit-cell parameters a = 118.5, b = 99.8, c = 123.2 Å, β = 117.6° (Shevtsov et al., 2008 ▶). The only homologue of known structure is B. subtilis anti-TRAP (PDB code 2bx9; Shevtsov et al., 2005 ▶), which is a dodecameric particle with cubic 23 point-group symmetry (Fig. 3 ▶ a). The sequence identity between B. subtilis and B. licheniformis anti-TRAP is 64%.


NCS-constrained exhaustive search using oligomeric models.

Isupov MN, Lebedev AA - Acta Crystallogr. D Biol. Crystallogr. (2007)

Solution of the structure of anti-TRAP from B. licheniformis. (a) Ribbon diagram of the dodecamer of anti-TRAP from B. subtilis. (b) Native Patterson synthesis, in which three strong non-equivalent non-origin peaks are present. (c) 120° and 180° sections of an SRF, indicating the orientations of twofold and threefold NCS axes. The trimeric search model (centre) was oriented so that its threefold molecular axis was aligned with the NCS threefold axis (red lines). TF searches were performed for a series of orientations related to that shown by a rotation around the molecular threefold axis by the variable angle χ. (d) The highest CC in the TF search is plotted as a function of χ. (e) The MR solution with four dodecamers in the asymmetric unit, which are related by the translational NCS. This figure was prepared using BOBSCRIPT, MOLREP, CCP4mg (Potterton et al., 2004 ▶) and R.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394828&req=5

fig3: Solution of the structure of anti-TRAP from B. licheniformis. (a) Ribbon diagram of the dodecamer of anti-TRAP from B. subtilis. (b) Native Patterson synthesis, in which three strong non-equivalent non-origin peaks are present. (c) 120° and 180° sections of an SRF, indicating the orientations of twofold and threefold NCS axes. The trimeric search model (centre) was oriented so that its threefold molecular axis was aligned with the NCS threefold axis (red lines). TF searches were performed for a series of orientations related to that shown by a rotation around the molecular threefold axis by the variable angle χ. (d) The highest CC in the TF search is plotted as a function of χ. (e) The MR solution with four dodecamers in the asymmetric unit, which are related by the translational NCS. This figure was prepared using BOBSCRIPT, MOLREP, CCP4mg (Potterton et al., 2004 ▶) and R.
Mentions: Anti-TRAP is a small protein of 53 amino acids which regulates the activity of tryptophan attenuation protein (TRAP; Antson et al., 1999 ▶) in Bacillus. Anti-TRAP from B. licheniformis was crystallized in space group P21, with unit-cell parameters a = 118.5, b = 99.8, c = 123.2 Å, β = 117.6° (Shevtsov et al., 2008 ▶). The only homologue of known structure is B. subtilis anti-TRAP (PDB code 2bx9; Shevtsov et al., 2005 ▶), which is a dodecameric particle with cubic 23 point-group symmetry (Fig. 3 ▶ a). The sequence identity between B. subtilis and B. licheniformis anti-TRAP is 64%.

Bottom Line: In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted.In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search.Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.

View Article: PubMed Central - HTML - PubMed

Affiliation: Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England. m.isupov@exeter.ac.uk

ABSTRACT
The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.

Show MeSH