1kn1: Difference between revisions

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1kn1.gif|left|200px]]<br /><applet load="1kn1" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1kn1, resolution 2.2&Aring;" />
-'''Crystal structure of allophycocyanin'''<br />
-==Overview==
+==Crystal structure of allophycocyanin==
-The crystal structure of allophycocyanin from red algae Porphyra yezoensis, (APC-PY) at 2.2-A resolution has been determined by the molecular, replacement method. The crystal belongs to space group R32 with cell, parameters a = b = 105.3 A, c = 189.4 A, alpha = beta = 90 degrees, gamma, = 120 degrees. After several cycles of refinement using program X-PLOR and, model building based on the electron density map, the crystallographic, R-factor converged to 19.3% (R-free factor is 26.9%) in the range of 10.0, to 2.2 A. The r.m.s. deviations of bond length and angles are 0.015 A and, 2.9 degrees, respectively. In the crystal, two APC-PY trimers associate, face to face into a hexamer. The assembly of two trimers within the, hexamer is similar to that of C-phycocyanin (C-PC) and R-phycoerythrin, (R-PE) hexamers, but the assembly tightness of the two trimers to the, hexamer is not so high as that in C-PC and R-PE hexamers. The, chromophore-protein interactions and possible pathway of energy transfer, were discussed. Phycocyanobilin 1alpha84 of APC-PY forms 5 hydrogen bonds, with 3 residues in subunit 2beta of another monomer. In R-PE and C-PC, chromophore 1alpha84 only forms 1 hydrogen bond with 2beta77 residue in, subunit 2beta. This result may support and explain great spectrum, difference exists between APC trimer and monomer.
+<StructureSection load='1kn1' size='340' side='right'caption='[[1kn1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kn1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neopyropia_yezoensis Neopyropia yezoensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KN1 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</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=1kn1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kn1 OCA], [https://pdbe.org/1kn1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kn1 RCSB], [https://www.ebi.ac.uk/pdbsum/1kn1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kn1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHAA_NEOYE PHAA_NEOYE] Light-harvesting photosynthetic tetrapyrrole chromophore-protein from the phycobiliprotein complex.
+== 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/kn/1kn1_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=1kn1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) at 2.2-A resolution has been determined by the molecular replacement method. The crystal belongs to space group R32 with cell parameters a = b = 105.3 A, c = 189.4 A, alpha = beta = 90 degrees, gamma = 120 degrees. After several cycles of refinement using program X-PLOR and model building based on the electron density map, the crystallographic R-factor converged to 19.3% (R-free factor is 26.9%) in the range of 10.0 to 2.2 A. The r.m.s. deviations of bond length and angles are 0.015 A and 2.9 degrees, respectively. In the crystal, two APC-PY trimers associate face to face into a hexamer. The assembly of two trimers within the hexamer is similar to that of C-phycocyanin (C-PC) and R-phycoerythrin (R-PE) hexamers, but the assembly tightness of the two trimers to the hexamer is not so high as that in C-PC and R-PE hexamers. The chromophore-protein interactions and possible pathway of energy transfer were discussed. Phycocyanobilin 1alpha84 of APC-PY forms 5 hydrogen bonds with 3 residues in subunit 2beta of another monomer. In R-PE and C-PC, chromophore 1alpha84 only forms 1 hydrogen bond with 2beta77 residue in subunit 2beta. This result may support and explain great spectrum difference exists between APC trimer and monomer.
-==About this Structure==
+Crystal structure of allophycocyanin from red algae Porphyra yezoensis at 2.2-A resolution.,Liu JY, Jiang T, Zhang JP, Liang DC J Biol Chem. 1999 Jun 11;274(24):16945-52. PMID:10358042<ref>PMID:10358042</ref>
-KN1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Porphyra_yezoensis Porphyra yezoensis] with BLA and CYC as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KN1 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of allophycocyanin from red algae Porphyra yezoensis at 2.2-A resolution., Liu JY, Jiang T, Zhang JP, Liang DC, J Biol Chem. 1999 Jun 11;274(24):16945-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10358042 10358042]
+</div>
-[[Category: Porphyra yezoensis]]
+<div class="pdbe-citations 1kn1" style="background-color:#fffaf0;"></div>
-[[Category: Protein complex]]
-[[Category: Chang, W.R.]]
-[[Category: Jiang, T.]]
-[[Category: Liang, D.C.]]
-[[Category: Liu, J.Y.]]
-[[Category: Zhang, J.P.]]
-[[Category: BLA]]
-[[Category: CYC]]
-[[Category: helix-turn-helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:22:37 2007''
+==See Also==
+*[[Allophycocyanin 3D structures|Allophycocyanin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Neopyropia yezoensis]]
+[[Category: Chang WR]]
+[[Category: Jiang T]]
+[[Category: Liang DC]]
+[[Category: Liu JY]]
+[[Category: Zhang JP]]