This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3kyv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3kyv" [edit=sysop:move=sysop])
Line 1: Line 1:
-
[[Image:3kyv.png|left|200px]]
+
==Denovo X-ray crystal structure determination of H-labeled perdeuterated rubredoxin at 100K==
 +
<StructureSection load='3kyv' size='340' side='right' caption='[[3kyv]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3kyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYV FirstGlance]. <br>
 +
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
 +
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kyu|3kyu]], [[3kyw|3kyw]], [[3kyx|3kyx]], [[3kyy|3kyy]]</td></tr>
 +
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rub, PF1282 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
 +
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kyv RCSB], [http://www.ebi.ac.uk/pdbsum/3kyv 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/ky/3kyv_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 locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.
-
<!--
+
Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.,Gardberg AS, Del Castillo AR, Weiss KL, Meilleur F, Blakeley MP, Myles DA Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):558-67. Epub 2010, Apr 21. PMID:20445231<ref>PMID:20445231</ref>
-
The line below this paragraph, containing "STRUCTURE_3kyv", creates the "Structure Box" on the page.
+
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
-
or leave the SCENE parameter empty for the default display.
+
-
-->
+
-
{{STRUCTURE_3kyv| PDB=3kyv | SCENE= }}
+
-
===Denovo X-ray crystal structure determination of H-labeled perdeuterated rubredoxin at 100K===
+
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
 
+
== References ==
-
<!--
+
<references/>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20445231}}, adds the Publication Abstract to the page
+
__TOC__
-
(as it appears on PubMed at http://www.pubmed.gov), where 20445231 is the PubMed ID number.
+
</StructureSection>
-
-->
+
-
{{ABSTRACT_PUBMED_20445231}}
+
-
 
+
-
==About this Structure==
+
-
[[3kyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYV OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:020445231</ref><references group="xtra"/>
+
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Gardberg, A S.]]
[[Category: Gardberg, A S.]]

Revision as of 09:48, 21 May 2014

Denovo X-ray crystal structure determination of H-labeled perdeuterated rubredoxin at 100K

3kyv, resolution 1.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kyv"
Views
Personal tools
Navigation
Toolbox