5h4f: Difference between revisions
New page: ==Structure of inorganic pyrophosphatase crystallised as a contaminant== <StructureSection load='5h4f' size='340' side='right' caption='5h4f, resolution 2.05Å' sc... |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Structure of inorganic pyrophosphatase crystallised as a contaminant== | ==Structure of inorganic pyrophosphatase crystallised as a contaminant== | ||
<StructureSection load='5h4f' size='340' side='right' caption='[[5h4f]], [[Resolution|resolution]] 2.05Å' scene=''> | <StructureSection load='5h4f' size='340' side='right'caption='[[5h4f]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5h4f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H4F OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5h4f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H4F FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5h4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h4f OCA], [https://pdbe.org/5h4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h4f RCSB], [https://www.ebi.ac.uk/pdbsum/5h4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h4f ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank. | |||
Structure determination of contaminant proteins using the MarathonMR procedure.,Hatti K, Biswas A, Chaudhary S, Dadireddy V, Sekar K, Srinivasan N, Murthy MR J Struct Biol. 2017 Mar;197(3):372-378. doi: 10.1016/j.jsb.2017.01.005. Epub 2017, Feb 3. PMID:28167161<ref>PMID:28167161</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5h4f" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Chaudhary | [[Category: Synthetic construct]] | ||
[[Category: Hatti | [[Category: Chaudhary S]] | ||
[[Category: Murthy | [[Category: Hatti K]] | ||
[[Category: Sekar | [[Category: Murthy MRN]] | ||
[[Category: Srinivasan | [[Category: Sekar K]] | ||
[[Category: Srinivasan N]] | |||
Latest revision as of 10:23, 9 August 2023
Structure of inorganic pyrophosphatase crystallised as a contaminantStructure of inorganic pyrophosphatase crystallised as a contaminant
Structural highlights
Publication Abstract from PubMedIn the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank. Structure determination of contaminant proteins using the MarathonMR procedure.,Hatti K, Biswas A, Chaudhary S, Dadireddy V, Sekar K, Srinivasan N, Murthy MR J Struct Biol. 2017 Mar;197(3):372-378. doi: 10.1016/j.jsb.2017.01.005. Epub 2017, Feb 3. PMID:28167161[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||