1kq4: Difference between revisions

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New page: left|200px<br /><applet load="1kq4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kq4, resolution 2.25Å" /> '''Crystal Structure of...
 
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[[Image:1kq4.gif|left|200px]]<br /><applet load="1kq4" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kq4, resolution 2.25&Aring;" />
'''Crystal Structure of Thy1-Complementing Protein (TM0449) from Thermotoga maritima at 2.25 A Resolution'''<br />


==Overview==
==CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION==
Structural genomics is emerging as a principal approach to define protein, structure-function relationships. To apply this approach on a genomic, scale, novel methods and technologies must be developed to determine large, numbers of structures. We describe the design and implementation of a, high-throughput structural genomics pipeline and its application to the, proteome of the thermophilic bacterium Thermotoga maritima. By using this, pipeline, we successfully cloned and attempted expression of 1,376 of the, predicted 1,877 genes (73%) and have identified crystallization conditions, for 432 proteins, comprising 23% of the T. maritima proteome., Representative structures from TM0423 glycerol dehydrogenase and TM0449, thymidylate synthase-complementing protein are presented as examples of, final outputs from the pipeline.
<StructureSection load='1kq4' size='340' side='right'caption='[[1kq4]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQ4 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]] 2.25&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1kq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kq4 OCA], [https://pdbe.org/1kq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kq4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kq4 ProSAT], [https://www.topsan.org/Proteins/JCSG/1kq4 TOPSAN]</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/kq/1kq4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1kq4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.


==About this Structure==
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.,Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9. Epub 2002 Aug 22. PMID:12193646<ref>PMID:12193646</ref>
1KQ4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with FAD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KQ4 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline., Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC, Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9. Epub 2002 Aug 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12193646 12193646]
</div>
[[Category: Single protein]]
<div class="pdbe-citations 1kq4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: JCSG, Joint.Center.for.Structural.Genomics.]]
[[Category: Miller MD]]
[[Category: Miller, M.D.]]
[[Category: Wilson IA]]
[[Category: Wilson, I.A.]]
[[Category: FAD]]
[[Category: flavin-adenine dinucleotide]]
[[Category: jcsg]]
[[Category: joint center for structural genomics]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomics]]
[[Category: thy1-complementing protein from thermotoga maritima]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:36:57 2007''

Latest revision as of 03:10, 21 November 2024

CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTIONCRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION

Structural highlights

1kq4 is a 4 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.25Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.,Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9. Epub 2002 Aug 22. PMID:12193646[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9. Epub 2002 Aug 22. PMID:12193646 doi:http://dx.doi.org/10.1073/pnas.142413399

1kq4, resolution 2.25Å

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