3kyw

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[[Image:3kyw.png|left|200px]]
 
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==Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K==
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The line below this paragraph, containing "STRUCTURE_3kyw", creates the "Structure Box" on the page.
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<StructureSection load='3kyw' size='340' side='right'caption='[[3kyw]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3kyw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KYW FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</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=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
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{{STRUCTURE_3kyw| PDB=3kyw | SCENE= }}
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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=3kyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyw OCA], [https://pdbe.org/3kyw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kyw RCSB], [https://www.ebi.ac.uk/pdbsum/3kyw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyw ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RUBR_PYRFU RUBR_PYRFU] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ky/3kyw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3kyw ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K===
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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>
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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 3kyw" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20445231}}, adds the Publication Abstract to the page
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*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20445231 is the PubMed ID number.
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*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
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== References ==
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{{ABSTRACT_PUBMED_20445231}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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[[3kyw]] 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=3KYW OCA].
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[[Category: Large Structures]]
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==Reference==
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<ref group="xtra">PMID:020445231</ref><references group="xtra"/>
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[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Gardberg, A S.]]
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[[Category: Gardberg AS]]
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[[Category: Electron transport]]
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[[Category: Iron]]
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[[Category: Metal-binding]]
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[[Category: Transport]]
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[[Category: Ultra-high resolution room-temperature]]
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Current revision

Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K

PDB ID 3kyw

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