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.


1oxd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:51, 17 April 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1oxd.jpg|left|200px]]
 
-
{{Structure
+
==Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins==
-
|PDB= 1oxd |SIZE=350|CAPTION= <scene name='initialview01'>1oxd</scene>, resolution 1.15&Aring;
+
<StructureSection load='1oxd' size='340' side='right'caption='[[1oxd]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NYC:(5Z)-5-(1H-INDOL-3-YLMETHYLENE)-4H-IMIDAZOL-4-ONE'>NYC</scene>
+
<table><tr><td colspan='2'>[[1oxd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cfp_marker_plasmid_pWM1009 Cfp marker plasmid pWM1009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OXD FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oxd OCA], [https://pdbe.org/1oxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oxd RCSB], [https://www.ebi.ac.uk/pdbsum/1oxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oxd ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1emb|1EMB]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oxd OCA], [http://www.ebi.ac.uk/pdbsum/1oxd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1oxd RCSB]</span>
+
== 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/ox/1oxd_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=1oxd ConSurf].
 +
<div style="clear:both"></div>
-
'''Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins'''
+
==See Also==
-
 
+
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Much effort has been dedicated to the design of significantly red shifted variants of the green fluorescent protein (GFP) from Aequoria victora (av). These approaches have been based on classical engineering with the 20 canonical amino acids. We report here an expansion of these efforts by incorporation of an amino substituted variant of tryptophan into the "cyan" GFP mutant, which turned it into a "gold" variant. This variant possesses a red shift in emission unprecedented for any avFP, similar to "red" FPs, but with enhanced stability and a very low aggregation tendency. An increasing number of non-natural amino acids are available for chromophore redesign (by engineering of the genetic code) and enable new general strategies to generate novel classes of tailor-made GFP proteins.
+
[[Category: Cfp marker plasmid pWM1009]]
-
 
+
[[Category: Large Structures]]
-
==About this Structure==
+
[[Category: Azim MK]]
-
1OXD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cfp_marker_plasmid_pwm1009 Cfp marker plasmid pwm1009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OXD OCA].
+
[[Category: Budisa N]]
-
 
+
[[Category: Holak TA]]
-
==Reference==
+
[[Category: Huber R]]
-
Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins., Bae JH, Rubini M, Jung G, Wiegand G, Seifert MH, Azim MK, Kim JS, Zumbusch A, Holak TA, Moroder L, Huber R, Budisa N, J Mol Biol. 2003 May 16;328(5):1071-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12729742 12729742]
+
[[Category: Hyun Bae J]]
-
[[Category: Cfp marker plasmid pwm1009]]
+
[[Category: Jung G]]
-
[[Category: Single protein]]
+
[[Category: Kim JS]]
-
[[Category: Azim, M K.]]
+
[[Category: Moroder L]]
-
[[Category: Bae, J Hyun.]]
+
[[Category: Rubini M]]
-
[[Category: Budisa, N.]]
+
[[Category: Seifert MH]]
-
[[Category: Holak, T A.]]
+
[[Category: Wiegand G]]
-
[[Category: Huber, R.]]
+
[[Category: Zumbusch A]]
-
[[Category: Jung, G.]]
+
-
[[Category: Kim, J S.]]
+
-
[[Category: Moroder, L.]]
+
-
[[Category: Rubini, M.]]
+
-
[[Category: Seifert, M H.]]
+
-
[[Category: Wiegand, G.]]
+
-
[[Category: Zumbusch, A.]]
+
-
[[Category: amino acid incorporation]]
+
-
[[Category: chromophore]]
+
-
[[Category: genetic code]]
+
-
[[Category: green fluorescent protein]]
+
-
[[Category: tryptophan]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:51:41 2008''
+

Current revision

Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins

PDB ID 1oxd

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/1oxd"
Personal tools