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2m30

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==Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods==
==Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods==
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<StructureSection load='2m30' size='340' side='right'caption='[[2m30]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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<StructureSection load='2m30' size='340' side='right'caption='[[2m30]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2m30]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M30 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2m30]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M30 FirstGlance]. <br>
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</td></tr><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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r1v|1r1v]], [[1r1u|1r1u]], [[2kjb|2kjb]], [[2kjc|2kjc]]</div></td></tr>
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<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>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">czrA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m30 OCA], [https://pdbe.org/2m30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m30 RCSB], [https://www.ebi.ac.uk/pdbsum/2m30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m30 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=2m30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m30 OCA], [https://pdbe.org/2m30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m30 RCSB], [https://www.ebi.ac.uk/pdbsum/2m30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m30 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/O85142_STAAU O85142_STAAU]
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Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.
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Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.,Chakravorty DK, Wang B, Lee CW, Guerra AJ, Giedroc DP, Merz KM Jr J Biomol NMR. 2013 Apr 23. PMID:23609042<ref>PMID:23609042</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2m30" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Arunkumar, A I]]
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[[Category: Staphylococcus aureus]]
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[[Category: Chakravorty, D K]]
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[[Category: Arunkumar AI]]
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[[Category: Giedroc, D P]]
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[[Category: Chakravorty DK]]
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[[Category: Guerra, A J]]
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[[Category: Giedroc DP]]
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[[Category: Kong, X]]
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[[Category: Guerra AJ]]
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[[Category: Lee, C I]]
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[[Category: Kong X]]
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[[Category: Merz, K M]]
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[[Category: Lee CI]]
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[[Category: Pennella, M]]
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[[Category: Merz Jr KM]]
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[[Category: Wang, B I]]
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[[Category: Pennella M]]
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[[Category: Metal ion refinement]]
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[[Category: Wang BI]]
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[[Category: Transcription repressor]]
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Current revision

Solution NMR refinement of a metal ion bound protein using quantum mechanical/molecular mechanical and molecular dynamics methods

PDB ID 2m30

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