2pk8: Difference between revisions

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OCA

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 ==Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus==
-<StructureSection load='2pk8' size='340' side='right' caption='[[2pk8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='2pk8' size='340' side='right'caption='[[2pk8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pk8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1she 1she]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PK8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1she 1she]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PK8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AUC:GOLD+(I)+CYANIDE+ION'>AUC</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF0899 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AUC:GOLD+(I)+CYANIDE+ION'>AUC</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pk8 OCA], [http://pdbe.org/2pk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pk8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pk8 ProSAT]</span></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=2pk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pk8 OCA], [https://pdbe.org/2pk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pk8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pk8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8U2E0_PYRFU Q8U2E0_PYRFU]
 == 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/pk/2pk8_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pk8_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 20: @@
 </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=2pk8 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been determined by the Southeast Collaboratory for Structural Genomics (http://www.secsg.org). The structure was solved using the SCA2Structure pipeline from multiple data sets and has been refined to 1.85 A against the highest resolution data set collected (a presumed gold derivative), with a crystallographic R factor of 21.0% and R(free) of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein.
-Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution.,Kelley LL, Dillard BD, Tempel W, Chen L, Shaw N, Lee D, Newton MG, Sugar FJ, Jenney FE Jr, Lee HS, Shah C, Poole FL 3rd, Adams MW, Richardson JS, Richardson DC, Liu ZJ, Wang BC, Rose J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jul 1;63(Pt, 7):549-52. Epub 2007 Jun 11. PMID:17620707<ref>PMID:17620707</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2pk8" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrfu]]
+[[Category: Large Structures]]
-[[Category: Adams, M W.W]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Chen, L]]
+[[Category: Adams MWW]]
-[[Category: Clancy-Kelley, L L]]
+[[Category: Chen L]]
-[[Category: Dillard, B D]]
+[[Category: Clancy-Kelley LL]]
-[[Category: III, F L.Poole]]
+[[Category: Dillard BD]]
-[[Category: Izumi, M]]
+[[Category: Izumi M]]
-[[Category: Jenny, F E]]
+[[Category: Jenny Jr FE]]
-[[Category: Lee, D]]
+[[Category: Lee D]]
-[[Category: Lee, H S]]
+[[Category: Lee HS]]
-[[Category: Liu, Z J]]
+[[Category: Liu ZJ]]
-[[Category: Richardson, D C]]
+[[Category: Poole III FL]]
-[[Category: Richardson, J S]]
+[[Category: Richardson DC]]
-[[Category: Rose, J P]]
+[[Category: Richardson JS]]
-[[Category: Structural genomic]]
+[[Category: Rose JP]]
-[[Category: Shah, A]]
+[[Category: Shah A]]
-[[Category: Shah, C]]
+[[Category: Shah C]]
-[[Category: Sugar, F J]]
+[[Category: Sugar FJ]]
-[[Category: Tempel, W]]
+[[Category: Tempel W]]
-[[Category: Wang, B-C]]
+[[Category: Wang B-C]]
-[[Category: Pf0899]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Pyrococcus furiosus]]
-[[Category: Secsg]]
-[[Category: Uncharacterized protein]]
-[[Category: Unknown function]]