View source for 1vk1


==Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001==
<StructureSection load='1vk1' size='340' side='right'caption='[[1vk1]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VK1 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]] 1.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1vk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk1 OCA], [https://pdbe.org/1vk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vk1 RCSB], [https://www.ebi.ac.uk/pdbsum/1vk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk1 ProSAT], [https://www.topsan.org/Proteins/SECSG/1vk1 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8U3S5_PYRFU Q8U3S5_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/vk/1vk1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vk1 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization RESULTS: Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. CONCLUSION: In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.,Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ BMC Struct Biol. 2007 Jul 7;7:46. PMID:17617922<ref>PMID:17617922</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1vk1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Adams MWW]]
[[Category: Brereton PS]]
[[Category: Chang J]]
[[Category: Chen L]]
[[Category: Izumi M]]
[[Category: Jenney Jr FE]]
[[Category: Lee D]]
[[Category: Liu ZJ]]
[[Category: Ng J]]
[[Category: Poole II FL]]
[[Category: Richardson DC]]
[[Category: Richardson JS]]
[[Category: Rose J]]
[[Category: Shah A]]
[[Category: Shah C]]
[[Category: Sugar FJ]]
[[Category: Tempel W]]
[[Category: Wang BC]]
[[Category: Yang H]]
[[Category: Zhao M]]