3qba
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3qba]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBA FirstGlance]. <br> | <table><tr><td colspan='2'>[[3qba]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBA 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">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.53Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCZ:2-DEOXYCYTIDINE'>DCZ</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</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=3qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qba OCA], [https://pdbe.org/3qba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qba RCSB], [https://www.ebi.ac.uk/pdbsum/3qba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qba 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=3qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qba OCA], [https://pdbe.org/3qba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qba RCSB], [https://www.ebi.ac.uk/pdbsum/3qba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qba ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. | ||
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| - | Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.,Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT Structure. 2011 Apr 13;19(4):523-33. PMID:21481775<ref>PMID:21481775</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 3qba" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Z-DNA|Z-DNA]] | *[[Z-DNA|Z-DNA]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Brunger | + | [[Category: Brunger AT]] |
| - | [[Category: Fenn | + | [[Category: Fenn TD]] |
| - | [[Category: Langan | + | [[Category: Langan P]] |
| - | [[Category: Mustyakimov | + | [[Category: Mustyakimov M]] |
| - | [[Category: Pande | + | [[Category: Pande VS]] |
| - | [[Category: Schnieders | + | [[Category: Schnieders MJ]] |
| - | [[Category: Wu | + | [[Category: Wu C]] |
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Current revision
Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)
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Categories: Large Structures | Brunger AT | Fenn TD | Langan P | Mustyakimov M | Pande VS | Schnieders MJ | Wu C
