3lo8: Difference between revisions
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==Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms== | |||
<StructureSection load='3lo8' size='340' side='right' caption='[[3lo8]], [[Resolution|resolution]] 1.05Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3lo8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LO8 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jb9|1jb9]]</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=3lo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lo8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lo8 RCSB], [http://www.ebi.ac.uk/pdbsum/3lo8 PDBsum]</span></td></tr> | |||
</table> | |||
== 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/lo/3lo8_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the phi/psi angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm. | |||
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.,Tronrud DE, Berkholz DS, Karplus PA Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):834-42. Epub 2010, Jun 19. PMID:20606264<ref>PMID:20606264</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Defensin|Defensin]] | *[[Defensin|Defensin]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Zea mays]] | [[Category: Zea mays]] | ||
[[Category: Faber, H R | [[Category: Faber, H R]] | ||
[[Category: Karplus, P A | [[Category: Karplus, P A]] | ||
[[Category: Electron transport]] | [[Category: Electron transport]] | ||
[[Category: Fad]] | [[Category: Fad]] | ||
Revision as of 06:31, 18 December 2014
Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms
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