1b8d: Difference between revisions
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== | ==CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN== | ||
<StructureSection load='1b8d' size='340' side='right'caption='[[1b8d]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1b8d]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Griffithsia_monilis Griffithsia monilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B8D 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]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=PEB:PHYCOERYTHROBILIN'>PEB</scene>, <scene name='pdbligand=PUB:PHYCOUROBILIN'>PUB</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=1b8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b8d OCA], [https://pdbe.org/1b8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b8d RCSB], [https://www.ebi.ac.uk/pdbsum/1b8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b8d ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PHEA_GRIMO PHEA_GRIMO] | |||
== 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/b8/1b8d_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=1b8d ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The structure of R-phycoerythrin (R-PE) from the red alga Griffithsia monilis was solved at 1.90-A resolution by molecular replacement, using the atomic coordinates of cyanobacterial phycocyanin from Fremyella diplosiphon as a model. The crystallographic R factor for the final model is 17.5% (Rfree 22.7%) for reflections in the range 100-1.90 A. The model consists of an (alphabeta)2 dimer with an internal noncrystallographic dyad and a fragment of the gamma-polypeptide. The alpha-polypeptide (164 amino acid residues) has two covalently bound phycoerythrobilins at positions alpha82 and alpha139. The beta-polypeptide (177 residues) has two phycoerythrobilins bound to residues beta82 and beta158 and one phycourobilin covalently attached to rings A and D at residues beta50 and beta61, respectively. The electron density of the gamma-polypeptide is mostly averaged out by threefold crystallographic symmetry, but a dipeptide (Gly-Tyr) and one single Tyr could be modeled. These two tyrosine residues of the gamma-polypeptide are in close proximity to the phycoerythrobilins at position beta82 of two symmetry-related beta-polypeptides and are related by the same noncrystallographic dyad as the (alphabeta)2 dimer. Possible energy transfer pathways are discussed briefly. | The structure of R-phycoerythrin (R-PE) from the red alga Griffithsia monilis was solved at 1.90-A resolution by molecular replacement, using the atomic coordinates of cyanobacterial phycocyanin from Fremyella diplosiphon as a model. The crystallographic R factor for the final model is 17.5% (Rfree 22.7%) for reflections in the range 100-1.90 A. The model consists of an (alphabeta)2 dimer with an internal noncrystallographic dyad and a fragment of the gamma-polypeptide. The alpha-polypeptide (164 amino acid residues) has two covalently bound phycoerythrobilins at positions alpha82 and alpha139. The beta-polypeptide (177 residues) has two phycoerythrobilins bound to residues beta82 and beta158 and one phycourobilin covalently attached to rings A and D at residues beta50 and beta61, respectively. The electron density of the gamma-polypeptide is mostly averaged out by threefold crystallographic symmetry, but a dipeptide (Gly-Tyr) and one single Tyr could be modeled. These two tyrosine residues of the gamma-polypeptide are in close proximity to the phycoerythrobilins at position beta82 of two symmetry-related beta-polypeptides and are related by the same noncrystallographic dyad as the (alphabeta)2 dimer. Possible energy transfer pathways are discussed briefly. | ||
Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution.,Ritter S, Hiller RG, Wrench PM, Welte W, Diederichs K J Struct Biol. 1999 Jun 15;126(2):86-97. PMID:10388620<ref>PMID:10388620</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1b8d" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Griffithsia monilis]] | [[Category: Griffithsia monilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Diederichs | [[Category: Diederichs K]] | ||
[[Category: Hiller | [[Category: Hiller RG]] | ||
[[Category: Ritter | [[Category: Ritter S]] | ||
[[Category: Welte | [[Category: Welte W]] | ||
[[Category: Wrench | [[Category: Wrench PM]] | ||
Latest revision as of 05:37, 9 August 2023
CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN
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