3ut8: Difference between revisions

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<StructureSection load='3ut8' size='340' side='right'caption='[[3ut8]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
<StructureSection load='3ut8' size='340' side='right'caption='[[3ut8]], [[Resolution|resolution]] 2.17&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ut8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acet2 Acet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UT8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UT8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ut8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UT8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UT8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.168&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ut4|3ut4]], [[3ut7|3ut7]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_2751 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 ACET2])</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=3ut8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ut8 OCA], [https://pdbe.org/3ut8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ut8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ut8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ut8 ProSAT]</span></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=3ut8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ut8 OCA], [https://pdbe.org/3ut8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ut8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ut8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ut8 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A3DJ21_ACET2 A3DJ21_ACET2]
BACKGROUND: Comparative genomic analysis has revealed that in each genome a large number of open reading frames have no homologues in other species. Such singleton genes have attracted the attention of biochemists and structural biologists as a potential untapped source of new folds. Cthe_2751 is a 15.8 kDa singleton from an anaerobic, hyperthermophile Clostridium thermocellum. To gain insights into the architecture of the protein and obtain clues about its function, we decided to solve the structure of Cthe_2751. RESULTS: The protein crystallized in 4 different space groups that diffracted X-rays to 2.37 A (P3(1)21), 2.17 A (P2(1)2(1)2(1)), 3.01 A (P4(1)22), and 2.03 A (C222(1)) resolution, respectively. Crystal packing analysis revealed that the 3-D packing of Cthe_2751 dimers in P4(1)22 and C222(1) is similar with only a rotational difference of 2.69 degrees around the C axes. A new method developed to quantify the differences in packing of dimers in crystals from different space groups corroborated the findings of crystal packing analysis. Cthe_2751 is an all alpha-helical protein with a central hydrophobic core providing thermal stability via pi:cation and pi: pi interactions. A ProFunc analysis retrieved a very low match with a splicing endonuclease, suggesting a role for the protein in the processing of nucleic acids. CONCLUSIONS: Non-Pfam singleton Cthe_2751 folds into a known all alpha-helical fold. The structure has increased sequence coverage of non-Pfam proteins such that more protein sequences can be amenable to modelling. Our work on crystal packing analysis provides a new method to analyze dimers of the protein crystallized in different space groups. The utility of such an analysis can be expanded to oligomeric structures of other proteins, especially receptors and signaling molecules, many of which are known to function as oligomers.
 
Structural view of a non pfam singleton and crystal packing analysis.,Cheng C, Shaw N, Zhang X, Zhang M, Ding W, Wang BC, Liu ZJ PLoS One. 2012;7(2):e31673. Epub 2012 Feb 20. PMID:22363703<ref>PMID:22363703</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ut8" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Acet2]]
[[Category: Acetivibrio thermocellus ATCC 27405]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cheng, C]]
[[Category: Cheng C]]
[[Category: Ding, W]]
[[Category: Ding W]]
[[Category: Liu, Z J]]
[[Category: Liu ZJ]]
[[Category: Shaw, N]]
[[Category: Shaw N]]
[[Category: Wang, B C]]
[[Category: Wang BC]]
[[Category: Zhang, M]]
[[Category: Zhang M]]
[[Category: Zhang, X]]
[[Category: Zhang X]]
[[Category: A non pfam singleton]]
[[Category: Crystal packing analysis]]
[[Category: Helical fold]]
[[Category: Unknown function]]
[[Category: Ytoplasm]]

Latest revision as of 11:38, 20 March 2024

Structural view of a non Pfam singleton and crystal packing analysisStructural view of a non Pfam singleton and crystal packing analysis

Structural highlights

3ut8 is a 2 chain structure with sequence from Acetivibrio thermocellus ATCC 27405. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.168Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A3DJ21_ACET2

3ut8, resolution 2.17Å

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

OCA
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