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| | ==RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR== | | ==RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR== |
| - | <StructureSection load='1arr' size='340' side='right'caption='[[1arr]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1arr' size='340' side='right'caption='[[1arr]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1arr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1arr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARR FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1arq|1arq]]</div></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1arr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arr OCA], [https://pdbe.org/1arr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1arr RCSB], [https://www.ebi.ac.uk/pdbsum/1arr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1arr ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1arr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arr OCA], [https://pdbe.org/1arr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1arr RCSB], [https://www.ebi.ac.uk/pdbsum/1arr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1arr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RARC_BPP22 RARC_BPP22]] This protein acts as a transcriptional repressor of its own gene arc and of gene ant.
| + | [https://www.uniprot.org/uniprot/RARC_BPP22 RARC_BPP22] This protein acts as a transcriptional repressor of its own gene arc and of gene ant. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpp22]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boelens, R]] | + | [[Category: Salmonella virus P22]] |
| - | [[Category: Bonvin, A M.J J]] | + | [[Category: Boelens R]] |
| - | [[Category: Breg, J N]] | + | [[Category: Bonvin AMJJ]] |
| - | [[Category: Burgering, M J.M]] | + | [[Category: Breg JN]] |
| - | [[Category: Kaptein, R]] | + | [[Category: Burgering MJM]] |
| - | [[Category: Vis, H]] | + | [[Category: Kaptein R]] |
| - | [[Category: Gene-regulating protein]]
| + | [[Category: Vis H]] |
| Structural highlights
Function
RARC_BPP22 This protein acts as a transcriptional repressor of its own gene arc and of gene ant.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bonvin AM, Vis H, Breg JN, Burgering MJ, Boelens R, Kaptein R. Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. J Mol Biol. 1994 Feb 11;236(1):328-41. PMID:8107113 doi:http://dx.doi.org/S0022-2836(84)71138-7
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