1d20
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(New page: 200px<br /><applet load="1d20" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d20" /> '''SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPER...)
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Revision as of 00:09, 25 November 2007
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SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA
Overview
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.
About this Structure
1D20 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
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