2q53: Difference between revisions

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New page: left|200px<br /> <applet load="2q53" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q53, resolution 2.010Å" /> '''Ensemble refinemen...
 
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[[Image:2q53.gif|left|200px]]<br />
<applet load="2q53" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2q53, resolution 2.010&Aring;" />
'''Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens'''<br />


==Overview==
==Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens==
X-ray crystallography typically uses a single set of coordinates and B, factors to describe macromolecular conformations. Refinement of multiple, copies of the entire structure has been previously used in specific cases, as an alternative means of representing structural flexibility. Here, we, systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of, the distributions of atomic positions in the simulated structures than, single-conformer refinements. Comparison of principal components, calculated from the refined ensembles and simulations shows that concerted, motions are captured locally, but that correlations dissipate over long, distances. Ensemble refinement is also used on 50 experimental structures, of varying resolution and leads to decreases in R(free) values, implying, that improvements in the representation of flexibility observed for the, simulated structures may apply to real structures. These gains are, essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from, ensemble refinement.
<StructureSection load='2q53' size='340' side='right'caption='[[2q53]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2q53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q53 FirstGlance]. <br>
2Q53 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q53 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]] 2.01&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2q53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q53 OCA], [https://pdbe.org/2q53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q53 RCSB], [https://www.ebi.ac.uk/pdbsum/2q53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q53 ProSAT]</span></td></tr>
Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17850744 17850744]
</table>
== Function ==
[https://www.uniprot.org/uniprot/GGCT_HUMAN GGCT_HUMAN] Catalyzes the formation of 5-oxoproline from gamma-glutamyl dipeptides and may play a significant role in glutathione homeostasis. Induces release of cytochrome c from mitochondria with resultant induction of apoptosis.<ref>PMID:16765912</ref> <ref>PMID:18515354</ref>
== 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/q5/2q53_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=2q53 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
[[Category: Kondrashov DA]]
[[Category: Jr., G.N.Phillips.]]
[[Category: Levin EJ]]
[[Category: Kondrashov, D.A.]]
[[Category: Phillips Jr GN]]
[[Category: Levin, E.J.]]
[[Category: Wesenberg GE]]
[[Category: Wesenberg, G.E.]]
[[Category: center for eukaryotic structural genomics]]
[[Category: cesg]]
[[Category: ensemble refinement]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: refinement methodology development]]
[[Category: structural genomics]]
[[Category: unknown function]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:29:43 2007''

Latest revision as of 14:20, 30 August 2023

Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiensEnsemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens

Structural highlights

2q53 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.01Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GGCT_HUMAN Catalyzes the formation of 5-oxoproline from gamma-glutamyl dipeptides and may play a significant role in glutathione homeostasis. Induces release of cytochrome c from mitochondria with resultant induction of apoptosis.[1] [2]

Evolutionary Conservation

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

References

  1. ↑ Masuda Y, Maeda S, Watanabe A, Sano Y, Aiuchi T, Nakajo S, Itabe H, Nakaya K. A novel 21-kDa cytochrome c-releasing factor is generated upon treatment of human leukemia U937 cells with geranylgeraniol. Biochem Biophys Res Commun. 2006 Jul 28;346(2):454-60. PMID:16765912 doi:http://dx.doi.org/S0006-291X(06)01180-6
  2. ↑ Oakley AJ, Yamada T, Liu D, Coggan M, Clark AG, Board PG. The identification and structural characterization of C7orf24 as gamma-glutamyl cyclotransferase. An essential enzyme in the gamma-glutamyl cycle. J Biol Chem. 2008 Aug 8;283(32):22031-42. Epub 2008 May 30. PMID:18515354 doi:10.1074/jbc.M803623200

2q53, resolution 2.01Å

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