1s3o: Difference between revisions

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New page: left|200px<br /> <applet load="1s3o" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s3o, resolution 2.47Å" /> '''Human mitochondrial...
 
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[[Image:1s3o.gif|left|200px]]<br />
<applet load="1s3o" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1s3o, resolution 2.47&Aring;" />
'''Human mitochondrial single strand DNA binding protein (hmSSB)'''<br />


==Overview==
==Human mitochondrial single strand DNA binding protein (hmSSB)==
The Protein Data Bank (PDB) is the single most important repository of, structural data for proteins and other biologically relevant molecules., Therefore, it is critically important to keep the PDB data, as much as, possible, error-free. In this study, we have analyzed PDB crystal, structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure, mapping errors. Using energy-based structure quality assessment coupled, with sequence analyses, we have found that there are at least five, OB-structures in the PDB that have regions where sequences have been, incorrectly mapped onto the structure. We have demonstrated that the, combination of these computation techniques is effective not only in, detecting sequence-structure mapping errors, but also in providing, guidance to correct them. Namely, we have used results of computational, analysis to direct a revision of X-ray data for one of the PDB entries, containing a fairly inconspicuous sequence-structure mapping error. The, revised structure has been deposited with the PDB. We suggest use of, computational energy assessment and sequence analysis techniques to, facilitate structure determination when homologs having known structure, are available to use as a reference. Such computational analysis may be, useful in either guiding the sequence-structure assignment process or, verifying the sequence mapping within poorly defined regions.
<StructureSection load='1s3o' size='340' side='right'caption='[[1s3o]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1s3o]] 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=1S3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S3O 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]] 2.47&#8491;</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=1s3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s3o OCA], [https://pdbe.org/1s3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s3o RCSB], [https://www.ebi.ac.uk/pdbsum/1s3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s3o ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SSBP_HUMAN SSBP_HUMAN] This protein binds preferentially and cooperatively to ss-DNA. Probably involved in mitochondrial DNA replication. Associates with mitochondrial DNA.
== 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/s3/1s3o_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=1s3o ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1S3O 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=1S3O OCA].
*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Sequence-structure mapping errors in the PDB: OB-fold domains., Venclovas C, Ginalski K, Kang C, Protein Sci. 2004 Jun;13(6):1594-602. Epub 2004 May 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15133161 15133161]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Ginalski, K.]]
[[Category: Ginalski K]]
[[Category: Kang, C.]]
[[Category: Kang C]]
[[Category: Venclovas, C.]]
[[Category: Venclovas C]]
[[Category: ob fold]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 19:10:11 2007''

Latest revision as of 08:28, 14 February 2024

Human mitochondrial single strand DNA binding protein (hmSSB)

1s3o, resolution 2.47Å

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