3bog: Difference between revisions

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{{Seed}}
[[Image:3bog.jpg|left|200px]]


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==Snow Flea Antifreeze Protein Quasi-racemate==
The line below this paragraph, containing "STRUCTURE_3bog", creates the "Structure Box" on the page.
<StructureSection load='3bog' size='340' side='right'caption='[[3bog]], [[Resolution|resolution]] 1.20&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'>[[3bog]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOG FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-->
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DAR:D-ARGININE'>DAR</scene>, <scene name='pdbligand=DAS:D-ASPARTIC+ACID'>DAS</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DHI:D-HISTIDINE'>DHI</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=DTH:D-THREONINE'>DTH</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=SYS:3-[(2-AMINO-2-OXOETHYL)SELANYL]-L-ALANINE'>SYS</scene></td></tr>
{{STRUCTURE_3bog|  PDB=3bog  |  SCENE=  }}
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pne|2pne]], [[3boi|3boi]]</div></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=3bog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bog OCA], [https://pdbe.org/3bog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bog RCSB], [https://www.ebi.ac.uk/pdbsum/3bog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bog ProSAT]</span></td></tr>
</table>
== 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/bo/3bog_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=3bog ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the chemically synthesized proteins d-sfAFP and l-sfAFP occurred much more readily than for l-sfAFP alone. More facile crystal formation also occurred from a quasi-racemic mixture of d-sfAFP and l-Se-sfAFP, a chemical protein analogue that contains an additional -SeCH2- moiety at one residue and thus differs slightly from the true enantiomer. Multiple wavelength anomalous dispersion (MAD) phasing from quasi-racemate crystals was then used to determine the X-ray structure of the sfAFP protein molecule. The resulting model was used to solve by molecular replacement the X-ray structure of l-sfAFP to a resolution of 0.98 A. The l-sfAFP molecule is made up of six antiparallel left-handed PPII helixes, stacked in two sets of three, to form a compact brick-like structure with one hydrophilic face and one hydrophobic face. This is a novel experimental protein structure and closely resembles a structural model proposed for sfAFP. These results illustrate the utility of total chemical synthesis combined with racemic crystallization and X-ray crystallography for determining the unknown structure of a protein.


===Snow Flea Antifreeze Protein Quasi-racemate===
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers.,Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, Kossiakoff AA, Kent SB J Am Chem Soc. 2008 Jul 30;130(30):9695-701. Epub 2008 Jul 4. PMID:18598029<ref>PMID:18598029</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3bog" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18598029}}, adds the Publication Abstract to the page
*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18598029 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18598029}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3BOG is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOG OCA].
[[Category: Dashnau, J]]
 
[[Category: Gates, Z P]]
==Reference==
[[Category: Kent, S B.H]]
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers., Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, Kossiakoff AA, Kent SB, J Am Chem Soc. 2008 Jul 30;130(30):9695-701. Epub 2008 Jul 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18598029 18598029]
[[Category: Kossiakoff, A A]]
[[Category: Protein complex]]
[[Category: Kurutz, J]]
[[Category: Dashnau, J.]]
[[Category: Pentelute, B L]]
[[Category: Gates, Z P.]]
[[Category: Tereshko, V]]
[[Category: Kossiakoff, A A.]]
[[Category: Vaderkooi, J M]]
[[Category: Kurutz, J.]]
[[Category: Pentelute, B L.]]
[[Category: S B.H., Kent.]]
[[Category: Tereshko, V.]]
[[Category: Vaderkooi, J M.]]
[[Category: Antifreeze protein]]
[[Category: Antifreeze protein]]
[[Category: Mirror image protein]]
[[Category: Mirror image protein]]
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[[Category: Racemic protein crystallography]]
[[Category: Racemic protein crystallography]]
[[Category: Sfafp]]
[[Category: Sfafp]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 24 10:37:39 2008''
Retrieved from "https://proteopedia.org/3bog"