1arr
From Proteopedia
(New page: 200px<br /><applet load="1arr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1arr" /> '''RELAXATION MATRIX REFINEMENT OF THE SOLUTION...) |
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| - | [[Image:1arr.gif|left|200px]]<br /><applet load="1arr" size=" | + | [[Image:1arr.gif|left|200px]]<br /><applet load="1arr" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1arr" /> | caption="1arr" /> | ||
'''RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR'''<br /> | '''RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The Arc repressor of Salmonella bacteriophage P22 is a dimeric | + | The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D NMR data using an "ensemble" iterative relaxation matrix approach (IRMA) followed by direct NOE refinement with DINOSAUR. A set of 51 structures was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-ups in H2O and 2H2O via relaxation matrix calculations from the ensemble of structures. Methyl group rotation, aromatic ring flaps and internal mobility effects (via order parameters obtained from a free molecular dynamics run in water) were included in these calculations. The best structures were finally refined with direct NOE constraints following a slow-cooling simulated annealing protocol. In this final refinement stage, theoretical NOE intensities were directly compared with the experimental data and forces were derived using a simple two-spin approximation for the gradient of the NOE function. Dynamic assignment was applied to the peaks involving unassigned diastereotopic groups. The structure is determined to a precision (r.m.s.d. from the average excluding the ill defined C and N-terminal region) of 0.55 and 1.10 A for backbone and all atoms, respectively. The final structures, with R factor values around 0.35, have good stereochemical qualities, contain an extensive network of hydrogen bonds consistent with the secondary structure elements and structural features in concordance with genetic data. The overall folding of the solution and crystal structures is the same. |
==About this Structure== | ==About this Structure== | ||
| - | 1ARR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_phage_py54 Yersinia phage py54]. Full crystallographic information is available from [http:// | + | 1ARR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_phage_py54 Yersinia phage py54]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARR OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Yersinia phage py54]] | [[Category: Yersinia phage py54]] | ||
[[Category: Boelens, R.]] | [[Category: Boelens, R.]] | ||
| - | [[Category: Bonvin, A | + | [[Category: Bonvin, A M.J J.]] |
| - | [[Category: Breg, J | + | [[Category: Breg, J N.]] |
| - | [[Category: Burgering, M | + | [[Category: Burgering, M J.M.]] |
[[Category: Kaptein, R.]] | [[Category: Kaptein, R.]] | ||
[[Category: Vis, H.]] | [[Category: Vis, H.]] | ||
[[Category: gene-regulating protein]] | [[Category: gene-regulating protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:47:39 2008'' |
Revision as of 09:47, 21 February 2008
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RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR
Overview
The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D NMR data using an "ensemble" iterative relaxation matrix approach (IRMA) followed by direct NOE refinement with DINOSAUR. A set of 51 structures was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-ups in H2O and 2H2O via relaxation matrix calculations from the ensemble of structures. Methyl group rotation, aromatic ring flaps and internal mobility effects (via order parameters obtained from a free molecular dynamics run in water) were included in these calculations. The best structures were finally refined with direct NOE constraints following a slow-cooling simulated annealing protocol. In this final refinement stage, theoretical NOE intensities were directly compared with the experimental data and forces were derived using a simple two-spin approximation for the gradient of the NOE function. Dynamic assignment was applied to the peaks involving unassigned diastereotopic groups. The structure is determined to a precision (r.m.s.d. from the average excluding the ill defined C and N-terminal region) of 0.55 and 1.10 A for backbone and all atoms, respectively. The final structures, with R factor values around 0.35, have good stereochemical qualities, contain an extensive network of hydrogen bonds consistent with the secondary structure elements and structural features in concordance with genetic data. The overall folding of the solution and crystal structures is the same.
About this Structure
1ARR is a Single protein structure of sequence from Yersinia phage py54. Full crystallographic information is available from OCA.
Reference
Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations., Bonvin AM, Vis H, Breg JN, Burgering MJ, Boelens R, Kaptein R, J Mol Biol. 1994 Feb 11;236(1):328-41. PMID:8107113
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