5it4: Difference between revisions

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==Crystal structure of Mycobacterium avium SerB2 mutant D343N==
==Crystal structure of Mycobacterium avium SerB2 mutant D343N==
<StructureSection load='5it4' size='340' side='right' caption='[[5it4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='5it4' size='340' side='right'caption='[[5it4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5it4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IT4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5it4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_avium_104 Mycobacterium avium 104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IT4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.102&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5is2|5is2]], [[5it0|5it0]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoserine_phosphatase Phosphoserine phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.3 3.1.3.3] </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=5it4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5it4 OCA], [https://pdbe.org/5it4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5it4 RCSB], [https://www.ebi.ac.uk/pdbsum/5it4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5it4 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5it4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5it4 OCA], [http://pdbe.org/5it4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5it4 RCSB], [http://www.ebi.ac.uk/pdbsum/5it4 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SERB_MYCA1 SERB_MYCA1]] Catalyzes the dephosphorylation of phosphoserine (P-Ser).
[https://www.uniprot.org/uniprot/SERB_MYCA1 SERB_MYCA1] Catalyzes the dephosphorylation of phosphoserine (P-Ser).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.


SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref>
==See Also==
 
*[[Phosphoserine phosphatase|Phosphoserine phosphatase]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5it4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Phosphoserine phosphatase]]
[[Category: Large Structures]]
[[Category: Ramachandran, R]]
[[Category: Mycobacterium avium 104]]
[[Category: Shree, S]]
[[Category: Ramachandran R]]
[[Category: Catalytic site mutant]]
[[Category: Shree S]]
[[Category: Had family]]
[[Category: Hydrolase]]

Latest revision as of 17:08, 30 August 2023

Crystal structure of Mycobacterium avium SerB2 mutant D343NCrystal structure of Mycobacterium avium SerB2 mutant D343N

Structural highlights

5it4 is a 1 chain structure with sequence from Mycobacterium avium 104. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.102Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SERB_MYCA1 Catalyzes the dephosphorylation of phosphoserine (P-Ser).

See Also

5it4, resolution 2.10Å

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