1x3e: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1x3e.gif|left|200px]]<br /><applet load="1x3e" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1x3e, resolution 2.15&Aring;" />
-'''Crystal structure of the single-stranded DNA-binding protein from Mycobacterium smegmatis'''<br />
-==Overview==
+==Crystal structure of the single-stranded DNA-binding protein from Mycobacterium smegmatis==
-The structure of Mycobacterium smegmatis single-stranded DNA-binding, protein (SSB) has been determined using three data sets collected from, related crystals. The structure is similar to that of its homologue from, Mycobacterium tuberculosis, indicating that the clamp arrangement that, stabilizes the dimer and the ellipsoidal shape of the tetramer are, characteristic features of mycobacterial SSBs. The central OB fold is, conserved in mycobacterial SSBs as well as those from Escherichia coli, Deinococcus radiodurans and human mitochondria. However, the quaternary, structure exhibits considerable variability. The observed plasticity of, the subunit is related to this variability. The crystal structures and, modelling provide a rationale for the variability. The strand involved in, the clamp mechanism, which leads to higher stability of the tetramer, appears to occur in all high-G+C Gram-positive bacteria. The higher, stability is perhaps required by these organisms. The mode of DNA binding, of mycobacterial SSBs is different from that of E. coli SSB partly on, account of the difference in the shape of the tetramers. Another, difference between the two modes is that the former contains additional, ionic interactions and is more susceptible to salt concentration.
+<StructureSection load='1x3e' size='340' side='right'caption='[[1x3e]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1x3e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X3E 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]] 2.15&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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=1x3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x3e OCA], [https://pdbe.org/1x3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x3e RCSB], [https://www.ebi.ac.uk/pdbsum/1x3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x3e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SSB_MYCS2 SSB_MYCS2]
+== 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/x3/1x3e_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=1x3e ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-X3E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis] with CD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1X3E OCA].
+*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association., Saikrishnan K, Manjunath GP, Singh P, Jeyakanthan J, Dauter Z, Sekar K, Muniyappa K, Vijayan M, Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1140-8. Epub 2005, Jul 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16041080 16041080]
+[[Category: Large Structures]]
-[[Category: Mycobacterium smegmatis]]
+[[Category: Mycolicibacterium smegmatis]]
-[[Category: Single protein]]
+[[Category: Dauter Z]]
-[[Category: Dauter, Z.]]
+[[Category: Jeyakanthan J]]
-[[Category: Jeyakanthan, J.]]
+[[Category: Manjunath GP]]
-[[Category: Manjunath, G.P.]]
+[[Category: Muniyappa K]]
-[[Category: Muniyappa, K.]]
+[[Category: Saikrishnan K]]
-[[Category: Saikrishnan, K.]]
+[[Category: Sekar K]]
-[[Category: Sekar, K.]]
+[[Category: Singh P]]
-[[Category: Singh, P.]]
+[[Category: Vijayan M]]
-[[Category: Vijayan, M.]]
-[[Category: CD]]
-[[Category: dna-binding protein]]
-[[Category: oligonucleotide binding fold]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:49:08 2007''