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==Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms== | ==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=''> | <StructureSection load='3lo8' size='340' side='right' caption='[[3lo8]], [[Resolution|resolution]] 1.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3lo8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3lo8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Maize Maize]. 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> | </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='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='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> | <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://pdbe.org/3lo8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lo8 RCSB], [http://www.ebi.ac.uk/pdbsum/3lo8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lo8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3lo8 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 26: | Line 27: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3lo8" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Maize]] | ||
[[Category: Faber, H R]] | [[Category: Faber, H R]] | ||
[[Category: Karplus, P A]] | [[Category: Karplus, P A]] | ||
Revision as of 11:21, 5 August 2016
Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 AngstromsCrystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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