This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1p7e

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1p7e.jpg|left|200px]]
+
{{Seed}}
 +
[[Image:1p7e.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1p7e| PDB=1p7e | SCENE= }}
{{STRUCTURE_1p7e| PDB=1p7e | SCENE= }}
-
'''GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings'''
+
===GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings===
-
==Overview==
+
<!--
-
NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity (&lt;omega&gt; = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.
+
The line below this paragraph, {{ABSTRACT_PUBMED_15369375}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 15369375 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_15369375}}
==About this Structure==
==About this Structure==
-
1P7E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7E OCA].
+
1P7E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7E OCA].
==Reference==
==Reference==
Line 27: Line 31:
[[Category: Ulmer, T S.]]
[[Category: Ulmer, T S.]]
[[Category: Immune system]]
[[Category: Immune system]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:46:44 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:37:48 2008''

Revision as of 00:37, 29 July 2008

Image:1p7e.png

Template:STRUCTURE 1p7e

GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings

Template:ABSTRACT PUBMED 15369375

About this Structure

1P7E is a Single protein structure of sequence from Bacteria. Full experimental information is available from OCA.

Reference

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy., Ulmer TS, Ramirez BE, Delaglio F, Bax A, J Am Chem Soc. 2003 Jul 30;125(30):9179-91. PMID:15369375

Page seeded by OCA on Tue Jul 29 03:37:48 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1p7e"
Personal tools