4um4: Difference between revisions
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New page: '''Unreleased structure''' The entry 4um4 is ON HOLD Authors: Campos-Acevedo, A.A., Rudino-Pinera, E. Description: STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPL... |
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The entry | ==STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH SULFATE== | ||
<StructureSection load='4um4' size='340' side='right'caption='[[4um4]], [[Resolution|resolution]] 2.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4um4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UM4 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]] 2.65Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4um4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4um4 OCA], [https://pdbe.org/4um4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4um4 RCSB], [https://www.ebi.ac.uk/pdbsum/4um4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4um4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/IPYR_ECOLI IPYR_ECOLI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The importance of sample homogeneity and purity in protein crystallization is essential to obtain high-quality diffracting crystals. Here, in an attempt to determine the crystal structure of thioredoxin 1 from whiteleg shrimp Litopenaeus vannamei (LvTrx), we inadvertently crystallized the hexameric inorganic pyrophosphatase of Escherichia coli (E-PPase) from a non-homogeneous sample product during the initial over-expression steps and partial purification of LvTrx. The structure determination and identification of the crystallized protein were derived from several clues: the failures in the Molecular Replacement (MR) trials using LvTrx coordinates as a search model, the unit cell parameters and space group determination, and essentially by the use of the program BALBES. After using the previously deposited E-PPase structure (PDB entry 1mjw) as a search model and the correct space group assignation, the MR showed an E-PPase complexed with SO4-2 with small changes in the sulfate ion binding region when it compares to previously deposited E-PPases in the PDB. This work stresses the importance of protein purity to avoid the risk of crystallizing a contaminant protein or how pure need to be a protein sample in order to increase the possibility to obtain crystals, but also serves as a reminder that crystallization is by itself a purification process and how the program BALBES can be useful in the crystal structure determination of previously deposited structures in the PDB. | |||
First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target?,Campos-Acevedo AA, Diaz-Vilchis A, Sotelo-Mundo RR, Rudino-Pinera E Biochem Biophys Rep. 2016 Oct 15;8:284-289. doi: 10.1016/j.bbrep.2016.09.011., eCollection 2016 Dec. PMID:28955968<ref>PMID:28955968</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4um4" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | |||
[[Category: Large Structures]] | |||
[[Category: Campos-Acevedo AA]] | |||
[[Category: Rudino-Pinera E]] | |||
