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1d20

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[[Image:1d20.gif|left|200px]]
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{{STRUCTURE_1d20| PDB=1d20 | SCENE= }}
{{STRUCTURE_1d20| PDB=1d20 | SCENE= }}
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'''SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA'''
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===SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA===
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==Overview==
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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.
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The line below this paragraph, {{ABSTRACT_PUBMED_2141998}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 2141998 is the PubMed ID number.
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{{ABSTRACT_PUBMED_2141998}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D20 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D20 OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Phage lambda half-operator]]
[[Category: Phage lambda half-operator]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:21:39 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:09:32 2008''

Revision as of 19:09, 30 June 2008

Image:1d20.png

Template:STRUCTURE 1d20

SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA

Template:ABSTRACT PUBMED 2141998

About this Structure

Full experimental 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

Page seeded by OCA on Mon Jun 30 22:09:32 2008

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