1eyx: Difference between revisions

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~~[[Image:1eyx.gif|left|200px]]<br /><applet load="1eyx" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="1eyx, resolution 2.25Å" />~~

~~'''CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS'''<br />~~

==~~Overview~~==

==CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS==

R-phycoerythrin, a light-harvesting component from the red algae, Gracilaria chilensis, was crystallized by vapour diffusion using ammonium, sulfate as precipitant agent. Red crystals grew after one week at 293 K, and diffracted to 2.70 A resolution. Three serial macroseeding assays were, necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x, 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron, radiation at beamline BM14 of the European Synchrotron Radiation Facility, (ESRF) at Grenoble, France and was used for structure determination. Data, were collected at 100 K to a completeness of 98.6%. The crystal was, trigonal, space group R3, with unit-cell parameters a = b = 187.3, c =, 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the, CCP4 suite of programs indicated that the crystal was twinned, ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe, using the R-phycoerythrin from Polysiphonia urceolata [Chang et al., (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to, overcome the twinning problem, SHELX97 was used for the crystallographic, refinement. The twin fraction was 0.48, indicating a nearly perfect, hemihedrally twinned crystal. The final R(work) and R(free) factors are, 0.16 and 0.25, respectively. All the residues and chromophores of the, alpha- and beta-chains are well defined in the electron-density maps. Some, residues belonging to the gamma-linker are also recognizable.

== Structural highlights ==

<table><tr><td colspan='2'>[[1eyx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agarophyton_chilense Agarophyton chilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EYX 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]] 2.25Å</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>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=PUB:PHYCOUROBILIN'>PUB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1eyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eyx OCA], [https://pdbe.org/1eyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eyx RCSB], [https://www.ebi.ac.uk/pdbsum/1eyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eyx ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/PHEA_AGACH PHEA_AGACH]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/1eyx_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=1eyx ConSurf].

== Publication Abstract from PubMed ==

R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 A resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final R(work) and R(free) factors are 0.16 and 0.25, respectively. All the residues and chromophores of the alpha- and beta-chains are well defined in the electron-density maps. Some residues belonging to the gamma-linker are also recognizable.

~~==About this Structure==~~

Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.,Contreras-Martel C, Martinez-Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):52-60. PMID:11134927<ref>PMID:11134927</ref>

~~1EYX is a [http://en.wikipedia~~.~~org/wiki/Protein_complex Protein complex]~~ structure of ~~sequences~~ from ~~[http~~:~~//en~~.~~wikipedia.org/wiki/Gracilaria_chilensis Gracilaria chilensis] with SO4~~, ~~BLA~~, ~~CYC and PUB as [http~~:~~//en~~.~~wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=1EYX OCA].~~

~~==Reference==~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~Crystallization and 2~~.~~2 A resolution structure~~ of ~~R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning~~.~~, Contreras~~-~~Martel C, Martinez~~-~~Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC, Acta Crystallogr D Biol Crystallogr. 2001 Jan~~;~~57(Pt 1):52-60. PMID:[http:~~//~~ispc.weizmann.ac.il~~/~~/pmbin/getpm?pmid=11134927 11134927]~~

</div>

[[Category: ~~Gracilaria chilensis~~]]

[[Category: ~~Protein complex~~]]

== References ==

[[Category: Bunster, M.]]

[[Category: Contreras-Martel, C.]]

__TOC__

[[Category: Fontecilla-Camps~~, J.C.~~]]

</StructureSection>

[[Category: Legrand, P.]]

[[Category: Agarophyton chilense]]

[[Category: Martinez-Oyanedel, J.]]

[[Category: Large Structures]]

[[Category: Piras, C.]]

[[Category: Bunster M]]

[[Category: Vernede, X.]]

[[Category: Contreras-Martel C]]

~~[[Category: BLA]]~~

[[Category: Fontecilla-Camps JC]]

~~[[Category: CYC]]~~

[[Category: Legrand P]]

~~[[Category: PUB]]~~

[[Category: Martinez-Oyanedel J]]

~~[[Category: SO4]]~~

[[Category: Piras C]]

~~[[Category: macroseeding]]~~

[[Category: Vernede X]]

~~[[Category: phycobiliprotein]]~~

~~[[Category: protein structure]]~~

~~[[Category: r-phycoerythrin]]~~

~~[[Category: red algae]]~~

~~[[Category: sequences]]~~

~~[[Category: twin]]~~

~~''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:26:52 2007''~~

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@@ Line 1: / Line 1: @@
-[[Image:1eyx.gif|left|200px]]<br /><applet load="1eyx" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1eyx, resolution 2.25&Aring;" />
-'''CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS==
-R-phycoerythrin, a light-harvesting component from the red algae, Gracilaria chilensis, was crystallized by vapour diffusion using ammonium, sulfate as precipitant agent. Red crystals grew after one week at 293 K, and diffracted to 2.70 A resolution. Three serial macroseeding assays were, necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x, 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron, radiation at beamline BM14 of the European Synchrotron Radiation Facility, (ESRF) at Grenoble, France and was used for structure determination. Data, were collected at 100 K to a completeness of 98.6%. The crystal was, trigonal, space group R3, with unit-cell parameters a = b = 187.3, c =, 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the, CCP4 suite of programs indicated that the crystal was twinned, ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe, using the R-phycoerythrin from Polysiphonia urceolata [Chang et al., (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to, overcome the twinning problem, SHELX97 was used for the crystallographic, refinement. The twin fraction was 0.48, indicating a nearly perfect, hemihedrally twinned crystal. The final R(work) and R(free) factors are, 0.16 and 0.25, respectively. All the residues and chromophores of the, alpha- and beta-chains are well defined in the electron-density maps. Some, residues belonging to the gamma-linker are also recognizable.
+<StructureSection load='1eyx' size='340' side='right'caption='[[1eyx]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eyx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agarophyton_chilense Agarophyton chilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EYX 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]] 2.25&#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>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=PUB:PHYCOUROBILIN'>PUB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1eyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eyx OCA], [https://pdbe.org/1eyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eyx RCSB], [https://www.ebi.ac.uk/pdbsum/1eyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eyx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHEA_AGACH PHEA_AGACH]
+== 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/ey/1eyx_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=1eyx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 A resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final R(work) and R(free) factors are 0.16 and 0.25, respectively. All the residues and chromophores of the alpha- and beta-chains are well defined in the electron-density maps. Some residues belonging to the gamma-linker are also recognizable.
-==About this Structure==
+Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.,Contreras-Martel C, Martinez-Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):52-60. PMID:11134927<ref>PMID:11134927</ref>
-EYX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Gracilaria_chilensis Gracilaria chilensis] with SO4, BLA, CYC and PUB as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EYX OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning., Contreras-Martel C, Martinez-Oyanedel J, Bunster M, Legrand P, Piras C, Vernede X, Fontecilla-Camps JC, Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):52-60. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11134927 11134927]
+</div>
-[[Category: Gracilaria chilensis]]
+<div class="pdbe-citations 1eyx" style="background-color:#fffaf0;"></div>
-[[Category: Protein complex]]
+== References ==
-[[Category: Bunster, M.]]
+<references/>
-[[Category: Contreras-Martel, C.]]
+__TOC__
-[[Category: Fontecilla-Camps, J.C.]]
+</StructureSection>
-[[Category: Legrand, P.]]
+[[Category: Agarophyton chilense]]
-[[Category: Martinez-Oyanedel, J.]]
+[[Category: Large Structures]]
-[[Category: Piras, C.]]
+[[Category: Bunster M]]
-[[Category: Vernede, X.]]
+[[Category: Contreras-Martel C]]
-[[Category: BLA]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: CYC]]
+[[Category: Legrand P]]
-[[Category: PUB]]
+[[Category: Martinez-Oyanedel J]]
-[[Category: SO4]]
+[[Category: Piras C]]
-[[Category: macroseeding]]
+[[Category: Vernede X]]
-[[Category: phycobiliprotein]]
-[[Category: protein structure]]
-[[Category: r-phycoerythrin]]
-[[Category: red algae]]
-[[Category: sequences]]
-[[Category: twin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:26:52 2007''