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.


1xfn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:07, 9 May 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1xfn.png|left|200px]]
 
-
<!--
+
==NMR structure of the ground state of the photoactive yellow protein lacking the N-terminal part==
-
The line below this paragraph, containing "STRUCTURE_1xfn", creates the "Structure Box" on the page.
+
<StructureSection load='1xfn' size='340' side='right'caption='[[1xfn]]' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1xfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XFN FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-
{{STRUCTURE_1xfn| PDB=1xfn | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xfn OCA], [https://pdbe.org/1xfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xfn RCSB], [https://www.ebi.ac.uk/pdbsum/1xfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xfn ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xf/1xfn_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xfn ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The N-terminally truncated variant of photoactive yellow protein (Delta25-PYP) undergoes a very similar photocycle as the corresponding wild-type protein (WT-PYP), although the lifetime of its light-illuminated (pB) state is much longer. This has allowed determination of the structure of both its dark- (pG) as well as its pB-state in solution by nuclear magnetic resonance (NMR) spectroscopy. The pG structure shows a well-defined fold, similar to WT-PYP and the X-ray structure of the pG state of Delta25-PYP. In the long-lived photocycle intermediate pB, the central beta sheet is still intact, as well as a small part of one alpha helix. The remainder of pB is unfolded and highly flexible, as evidenced by results from proton-deuterium exchange and NMR relaxation studies. Thus, the partially unfolded nature of the presumed signaling state of PYP in solution, as suggested previously, has now been structurally demonstrated.
-
===NMR structure of the ground state of the photoactive yellow protein lacking the N-terminal part===
+
The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein.,Bernard C, Houben K, Derix NM, Marks D, van der Horst MA, Hellingwerf KJ, Boelens R, Kaptein R, van Nuland NA Structure. 2005 Jul;13(7):953-62. PMID:16004868<ref>PMID:16004868</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_16004868}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1xfn" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 16004868 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16004868}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1XFN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XFN OCA].
+
-
 
+
-
==Reference==
+
-
The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein., Bernard C, Houben K, Derix NM, Marks D, van der Horst MA, Hellingwerf KJ, Boelens R, Kaptein R, van Nuland NA, Structure. 2005 Jul;13(7):953-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16004868 16004868]
+
[[Category: Halorhodospira halophila]]
[[Category: Halorhodospira halophila]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bernard, C.]]
+
[[Category: Bernard C]]
-
[[Category: Boelens, R.]]
+
[[Category: Boelens R]]
-
[[Category: Derix, N M.]]
+
[[Category: Derix NM]]
-
[[Category: Hellingwerf, K J.]]
+
[[Category: Hellingwerf KJ]]
-
[[Category: Horst, M A.van der.]]
+
[[Category: Houben K]]
-
[[Category: Houben, K.]]
+
[[Category: Kaptein R]]
-
[[Category: Kaptein, R.]]
+
[[Category: Marks D]]
-
[[Category: Marks, D.]]
+
[[Category: Van Nuland NA]]
-
[[Category: Nuland, N A.van.]]
+
[[Category: Van der Horst MA]]
-
[[Category: Pas domain]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:46:30 2008''
+

Current revision

NMR structure of the ground state of the photoactive yellow protein lacking the N-terminal part

PDB ID 1xfn

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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