2pk8: Difference between revisions

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-[[Image:2pk8.gif|left|200px]]<br /><applet load="2pk8" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2pk8, resolution 1.85&Aring;" />
-'''Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus'''<br />
-==Overview==
+==Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus==
-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.
+<StructureSection load='2pk8' size='340' side='right'caption='[[2pk8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<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>
-PK8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638] with <scene name='pdbligand=AUC:'>AUC</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1SHE. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PK8 OCA].
+</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='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>
-==Reference==
+<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>
-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 Crystallograph Sect F Struct Biol Cryst Commun. 2007 Jul 1;63(Pt, 7):549-52. Epub 2007 Jun 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17620707 17620707]
+</table>
-[[Category: Pyrococcus furiosus dsm 3638]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/Q8U2E0_PYRFU Q8U2E0_PYRFU]
-[[Category: Adams, M.W.W.]]
+== Evolutionary Conservation ==
-[[Category: Chen, L.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Clancy-Kelley, L.L.]]
+Check<jmol>
-[[Category: Dillard, B.D.]]
+  <jmolCheckbox>
-[[Category: III, F.L.Poole.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pk8_consurf.spt"</scriptWhenChecked>
-[[Category: Izumi, M.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Jr., F.E.Jenny.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Lee, D.]]
+  </jmolCheckbox>
-[[Category: Lee, H.S.]]
+</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].
-[[Category: Liu, Z.J.]]
+<div style="clear:both"></div>
-[[Category: Richardson, D.C.]]
+__TOC__
-[[Category: Richardson, J.S.]]
+</StructureSection>
-[[Category: Rose, J.P.]]
+[[Category: Large Structures]]
-[[Category: SECSG, Southeast.Collaboratory.for.Structural.Genomics.]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Shah, A.]]
+[[Category: Adams MWW]]
-[[Category: Shah, C.]]
+[[Category: Chen L]]
-[[Category: Sugar, F.J.]]
+[[Category: Clancy-Kelley LL]]
-[[Category: Tempel, W.]]
+[[Category: Dillard BD]]
-[[Category: Wang, B-C.]]
+[[Category: Izumi M]]
-[[Category: AUC]]
+[[Category: Jenny Jr FE]]
-[[Category: pf0899]]
+[[Category: Lee D]]
-[[Category: protein structure initiative]]
+[[Category: Lee HS]]
-[[Category: psi]]
+[[Category: Liu ZJ]]
-[[Category: pyrococcus furiosus]]
+[[Category: Poole III FL]]
-[[Category: secsg]]
+[[Category: Richardson DC]]
-[[Category: southeast collaboratory for structural genomics]]
+[[Category: Richardson JS]]
-[[Category: structural genomics]]
+[[Category: Rose JP]]
-[[Category: uncharacterized protein]]
+[[Category: Shah A]]
+[[Category: Shah C]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:23:03 2008''
+[[Category: Sugar FJ]]
+[[Category: Tempel W]]
+[[Category: Wang B-C]]