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| | ==SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA== | | ==SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA== |
| - | <StructureSection load='1d20' size='340' side='right' caption='[[1d20]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1d20' size='340' side='right'caption='[[1d20]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1d20]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D20 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1d20]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D20 FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d20 RCSB], [http://www.ebi.ac.uk/pdbsum/1d20 PDBsum]</span></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=1d20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d20 OCA], [https://pdbe.org/1d20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d20 RCSB], [https://www.ebi.ac.uk/pdbsum/1d20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d20 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1d20" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baleja, J D]] | + | [[Category: Large Structures]] |
| - | [[Category: Sykes, B D]] | + | [[Category: Baleja JD]] |
| - | [[Category: Dna]] | + | [[Category: Sykes BD]] |
| - | [[Category: Double helix]]
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| - | [[Category: Phage lambda half-operator]]
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| Structural highlights
Publication Abstract from PubMed
The structure of a DNA decamer comprising the left half of the OR3 operator from bacteriophage lambda is determined in solution by using nuclear magnetic resonance spectroscopy and restrained molecular mechanics calculations. Nuclear magnetic resonance assignments for nonexchangeable protons are obtained by two-dimensional correlated and nuclear Overhauser effect (NOE) spectroscopies. Exchangeable proton resonances are assigned by one-dimensional NOE experiments. Coupling constant measurements from one- and two-dimensional experiments are used to determine approximate dihedral angles within the deoxyribose ring. Distances between protons are estimated by extrapolating distances derived from the time-dependent NOE intensities to initial mixing times. The sets of dihedral angles and distances form a basis for structure determination by restrained molecular dynamics. Separate runs start from classical A and from B DNA and converge to essentially identical structures (atomic root mean square difference of 0.8 A). The structures are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated by using a full matrix analysis procedure. Final NOE residual (R) factors were less than 0.19. The resultant structures are generally B type in character, but display local sequence-dependent variations in dihedral angles and in the spatial arrangement of adjacent base pairs. Although the entire structure exhibits a small bend, the central core of the half-operator, which comprises the sequence-specific recognition site for cro repressor, is straight.
Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement.,Baleja JD, Pon RT, Sykes BD Biochemistry. 1990 May 22;29(20):4828-39. PMID:2141998[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Baleja JD, Pon RT, Sykes BD. Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement. Biochemistry. 1990 May 22;29(20):4828-39. PMID:2141998
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