3md7: Difference between revisions

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{{Seed}}
[[Image:3md7.jpg|left|200px]]


<!--
==Crystal structure of a beta-lactamase-like protein bound to GMP from brucella melitensis==
The line below this paragraph, containing "STRUCTURE_3md7", creates the "Structure Box" on the page.
<StructureSection load='3md7' size='340' side='right'caption='[[3md7]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3md7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_abortus_2308 Brucella abortus 2308]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MD7 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.27&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
{{STRUCTURE_3md7|  PDB=3md7  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3md7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3md7 OCA], [https://pdbe.org/3md7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3md7 RCSB], [https://www.ebi.ac.uk/pdbsum/3md7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3md7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q2YQ74_BRUA2 Q2YQ74_BRUA2]
== 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/md/3md7_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3md7 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of a beta-lactamase-like protein from Brucella melitensis was initially solved by SAD phasing from an in-house data set collected on a crystal soaked with iodide. A high-resolution data set was collected at a synchroton at the Se edge wavelength, which also provided an independent source of phasing using a small anomalous signal from metal ions in the active site. Comparisons of anomalous peak heights at various wavelengths allowed the identification of the active-site metal ions as manganese. In the native data set a partially occupied GMP could be identified. When co-crystallized with AMPPNP or GMPPNP, clear density for the hydrolyzed analogs was observed, providing hints to the function of the protein.


===Crystal structure of a beta-lactamase-like protein bound to GMP from brucella melitensis===
BrabA.11339.a: anomalous diffraction and ligand binding guide towards the elucidation of the function of a `putative beta-lactamase-like protein' from Brucella melitensis.,Abendroth J, Sankaran B, Edwards TE, Gardberg AS, Dieterich S, Bhandari J, Napuli AJ, Van Voorhis WC, Staker BL, Myler PJ, Stewart LJ Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Sep 1;67(Pt, 9):1106-12. Epub 2011 Aug 16. PMID:21904058<ref>PMID:21904058</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3MD7 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brucella_abortus Brucella abortus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MD7 OCA].
<div class="pdbe-citations 3md7" style="background-color:#fffaf0;"></div>
[[Category: Brucella abortus]]
== References ==
[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
<references/>
[[Category: Beta-lactamase like]]
__TOC__
[[Category: Hydrolase]]
</StructureSection>
[[Category: Seattle structural genomics center for infectious disease]]
[[Category: Brucella abortus 2308]]
[[Category: Ssgcid]]
[[Category: Large Structures]]
[[Category: Structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 11:10:42 2010''

Latest revision as of 13:17, 1 July 2026

Crystal structure of a beta-lactamase-like protein bound to GMP from brucella melitensis

3md7, resolution 1.27Å

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