2pk8: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2pk8.gif|left|200px]]
-<!--
+==Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus==
-The line below this paragraph, containing "STRUCTURE_2pk8", creates the "Structure Box" on the page.
+<StructureSection load='2pk8' size='340' side='right'caption='[[2pk8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_2pk8|  PDB=2pk8  |  SCENE=  }}
+<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>
-'''Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus'''
+== Function ==
+[https://www.uniprot.org/uniprot/Q8U2E0_PYRFU Q8U2E0_PYRFU]
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pk8_consurf.spt"</scriptWhenChecked>
-PK8 is a [[Single protein]] structure of sequence from [http://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].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17620707 17620707]
+</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: Pyrococcus furiosus dsm 3638]]
+<div style="clear:both"></div>
-[[Category: Single protein]]
+__TOC__
-[[Category: Adams, M W.W.]]
+</StructureSection>
-[[Category: Chen, L.]]
+[[Category: Large Structures]]
-[[Category: Clancy-Kelley, L L.]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Dillard, B D.]]
+[[Category: Adams MWW]]
-[[Category: III, F L.Poole.]]
+[[Category: Chen L]]
-[[Category: Izumi, M.]]
+[[Category: Clancy-Kelley LL]]
-[[Category: Jr., F E.Jenny.]]
+[[Category: Dillard BD]]
-[[Category: Lee, D.]]
+[[Category: Izumi M]]
-[[Category: Lee, H S.]]
+[[Category: Jenny Jr FE]]
-[[Category: Liu, Z J.]]
+[[Category: Lee D]]
-[[Category: Richardson, D C.]]
+[[Category: Lee HS]]
-[[Category: Richardson, J S.]]
+[[Category: Liu ZJ]]
-[[Category: Rose, J P.]]
+[[Category: Poole III FL]]
-[[Category: SECSG, Southeast Collaboratory for Structural Genomics.]]
+[[Category: Richardson DC]]
-[[Category: Shah, A.]]
+[[Category: Richardson JS]]
-[[Category: Shah, C.]]
+[[Category: Rose JP]]
-[[Category: Sugar, F J.]]
+[[Category: Shah A]]
-[[Category: Tempel, W.]]
+[[Category: Shah C]]
-[[Category: Wang, B-C.]]
+[[Category: Sugar FJ]]
-[[Category: Pf0899]]
+[[Category: Tempel W]]
-[[Category: Protein structure initiative]]
+[[Category: Wang B-C]]
-[[Category: Psi]]
-[[Category: Pyrococcus furiosus]]
-[[Category: Secsg]]
-[[Category: Southeast collaboratory for structural genomic]]
-[[Category: Structural genomic]]
-[[Category: Uncharacterized protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 13:17:04 2008''