We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

1arr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1arr.gif|left|200px]]
+
{{Seed}}
 +
[[Image:1arr.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1arr| PDB=1arr | SCENE= }}
{{STRUCTURE_1arr| PDB=1arr | SCENE= }}
-
'''RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR'''
+
===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.
+
The line below this paragraph, {{ABSTRACT_PUBMED_8107113}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 8107113 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_8107113}}
==About this Structure==
==About this Structure==
-
1ARR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p22 Enterobacteria phage p22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARR OCA].
+
1ARR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p22 Enterobacteria phage p22]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARR OCA].
==Reference==
==Reference==
Line 29: Line 33:
[[Category: Vis, H.]]
[[Category: Vis, H.]]
[[Category: Gene-regulating protein]]
[[Category: Gene-regulating protein]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:37:43 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:28:59 2008''

Revision as of 14:29, 30 June 2008

Image:1arr.png

Template:STRUCTURE 1arr

RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR

Template:ABSTRACT PUBMED 8107113

About this Structure

1ARR is a Single protein structure of sequence from Enterobacteria phage p22. Full experimental 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

Page seeded by OCA on Mon Jun 30 17:28:59 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1arr"
Personal tools