2fl1: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2fl1.png|left|200px]]
-{{STRUCTURE_2fl1|  PDB=2fl1  |  SCENE=  }}
+==Crystal structure of red fluorescent protein from Zoanthus, zRFP574, at 2.4A resolution==
+<StructureSection load='2fl1' size='340' side='right'caption='[[2fl1]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fl1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoanthus_sp. Zoanthus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FL1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FL1 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYG:[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>XYG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fl1 OCA], [https://pdbe.org/2fl1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fl1 RCSB], [https://www.ebi.ac.uk/pdbsum/2fl1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fl1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8T4U4_9CNID Q8T4U4_9CNID]
+== 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/fl/2fl1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2fl1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of the red fluorescent protein (RFP) zRFP574 from the button polyp Zoanthus sp. (two dimers per asymmetric unit, 231 x 4 amino acids) has been determined at 2.4 A resolution in space group C222(1). The crystal structure, refined to a crystallographic R factor of 0.203 (R(free) = 0.249), adopts the beta-barrel fold composed of 11 strands similar to that of the yellow fluorescent protein zYFP538. The zRFP574 chromophore, originating from the protein sequence Asp66-Tyr67-Gly68, has a two-ring structure typical of GFP-like proteins. The bond geometry of residue 66 shows the strong tendency of the corresponding C(alpha) atom to sp(2) hybridization as a consequence of N-acylimine bond formation. The zRFP574 chromophore contains the 65-66 cis-peptide bond characteristic of red fluorescent proteins. The chromophore phenolic ring adopts a cis conformation coplanar with the imidazolinone ring. The crystallographic study has revealed an unexpected chemical feature of the internal chromophore. A decarboxylated side chain of the chromophore-forming residue Asp66 has been observed in the structure. This additional post-translational modification is likely to play a key role in the bathochromic shift of the zRFP574 spectrum.
-===Crystal structure of red fluorescent protein from Zoanthus, zRFP574, at 2.4A resolution===
+Structure of a red fluorescent protein from Zoanthus, zRFP574, reveals a novel chromophore.,Pletneva N, Pletnev S, Tikhonova T, Popov V, Martynov V, Pletnev V Acta Crystallogr D Biol Crystallogr. 2006 May;62(Pt 5):527-32. Epub 2006, Apr 19. PMID:16627946<ref>PMID:16627946</ref>
-{{ABSTRACT_PUBMED_16627946}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2fl1" style="background-color:#fffaf0;"></div>
-[[2fl1]] is a 4 chain structure of [[Alyssa Marsico/Sandbox 1]], [[Devon McCarthy/Sandbox 1]], [[Green Fluorescent Protein]], [[Sandbox104]] and [[User:Joanne Lau/Sandbox 5]] with sequence from [http://en.wikipedia.org/wiki/Zoanthus_sp. Zoanthus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FL1 OCA].
 ==See Also==
-*[[Alyssa Marsico/Sandbox 1|Alyssa Marsico/Sandbox 1]]
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-*[[Devon McCarthy/Sandbox 1|Devon McCarthy/Sandbox 1]]
+== References ==
-*[[Green Fluorescent Protein|Green Fluorescent Protein]]
+<references/>
-*[[Sandbox104|Sandbox104]]
+__TOC__
-*[[User:Joanne Lau/Sandbox 5|User:Joanne Lau/Sandbox 5]]
+</StructureSection>
+[[Category: Large Structures]]
-==Reference==
+[[Category: Zoanthus sp]]
-<ref group="xtra">PMID:016627946</ref><references group="xtra"/>
+[[Category: Martynov V]]
-[[Category: Zoanthus sp.]]
+[[Category: Pletnev S]]
-[[Category: Martynov, V.]]
+[[Category: Pletnev V]]
-[[Category: Pletnev, S.]]
+[[Category: Pletneva N]]
-[[Category: Pletnev, V.]]
+[[Category: Popov B]]
-[[Category: Pletneva, N.]]
+[[Category: Tikhonova T]]
-[[Category: Popov, B.]]
-[[Category: Tikhonova, T.]]
-[[Category: Beta barrel]]
-[[Category: Beta-can fold]]
-[[Category: Button polyp]]
-[[Category: Chromophore]]
-[[Category: Emission maximum 574nm]]
-[[Category: Fluorescent marker]]
-[[Category: Fluorescent protein]]
-[[Category: Intersubunit interface]]
-[[Category: Red fluorescent protein]]
-[[Category: Tightly packed tetramer]]
-[[Category: Zoanthus sp.]]
-[[Category: Zrfp574]]