1xmz: Difference between revisions

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-{{Seed}}
-[[Image:1xmz.png|left|200px]]
-<!--
+==Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata==
-The line below this paragraph, containing "STRUCTURE_1xmz", creates the "Structure Box" on the page.
+<StructureSection load='1xmz' size='340' side='right'caption='[[1xmz]], [[Resolution|resolution]] 1.38&Aring;' 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'>[[1xmz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Anemonia_sulcata Anemonia sulcata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XMZ 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">X-ray diffraction, [[Resolution|Resolution]] 1.38&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CRK:4-{(Z)-[2-[3-(METHYLSULFANYL)PROPANOYL]-5-OXO-1-(2-OXOETHYL)-1,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE]METHYL}BENZENOLATE'>CRK</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-{{STRUCTURE_1xmz|  PDB=1xmz  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xmz OCA], [https://pdbe.org/1xmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xmz RCSB], [https://www.ebi.ac.uk/pdbsum/1xmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xmz ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NFCP_ANESU NFCP_ANESU] Pigment protein that is intensely purple in color.<ref>PMID:10852900</ref>
+== 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/xm/1xmz_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=1xmz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+When the nonfluorescent chromoprotein asFP595 from Anemonia sulcata is subjected to sufficiently intense illumination near the absorbance maximum (lambda(abs)(max) = 568 nm), it undergoes a remarkable transition, termed "kindling", to a long-lived fluorescent state (lambda(em)(max) = 595 nm). In the dark recovery phase, the kindled state relaxes thermally on a time scale of seconds or can instantly be reverted upon illumination at 450 nm. The kindling phenomenon is enhanced by the Ala143 --&gt; Gly point mutation, which slows the dark recovery time constant to 100 s at room temperature and increases the fluorescence quantum yield. To investigate the chemical nature of the chromophore and the possible role of chromophore isomerization in the kindling phenomenon, we determined the crystal structure of the "kindling fluorescent protein" asFP595-A143G (KFP) in the dark-adapted state at 1.38 A resolution and 100 K. The chromophore, derived from the Met63-Tyr64-Gly65 tripeptide, closely resembles that of the nonfluorescent chromoprotein Rtms5 in that the configuration is trans about the methylene bridge and there is substantial distortion from planarity. Unlike in Rtms5, in the native protein the polypeptide backbone is cleaved between Cys62 and Met63. The size and shape of the chromophore pocket suggest that the cis isomer of the chromophore could also be accommodated. Within the pocket, partially disordered His197 displays two conformations, which may constitute a binary switch that stabilizes different chromophore configurations. The energy barrier for thermal relaxation was found by Arrhenius plot analysis to be approximately 71 kJ/mol, somewhat higher than the value of approximately 55 kJ/mol observed for cis-trans isomerization of a model chromophore in solution.
-===Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata===
+Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution.,Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ Biochemistry. 2005 Apr 19;44(15):5774-87. PMID:15823036<ref>PMID:15823036</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xmz" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15823036}}, adds the Publication Abstract to the page
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15823036 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15823036}}
+__TOC__
+</StructureSection>
-==About this Structure==
-XMZ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Anemonia_sulcata Anemonia sulcata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XMZ OCA].
-==Reference==
-<ref group="xtra">PMID:15823036</ref><references group="xtra"/>
 [[Category: Anemonia sulcata]]
-[[Category: Anstrom, D M.]]
+[[Category: Large Structures]]
-[[Category: Chudakov, D M.]]
+[[Category: Anstrom DM]]
-[[Category: Kallio, K.]]
+[[Category: Chudakov DM]]
-[[Category: Leary, S O.]]
+[[Category: Kallio K]]
-[[Category: Quillin, M L.]]
+[[Category: O'Leary S]]
-[[Category: Remington, S J.]]
+[[Category: Quillin ML]]
-[[Category: Shu, X.]]
+[[Category: Remington SJ]]
-[[Category: Ascp595]]
+[[Category: Shu X]]
-[[Category: Chromophore structure]]
-[[Category: Fluorescent protein]]
-[[Category: Luminescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  1 09:46:50 2009''