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1yk4

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{{Seed}}
 
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[[Image:1yk4.png|left|200px]]
 
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==Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S==
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The line below this paragraph, containing "STRUCTURE_1yk4", creates the "Structure Box" on the page.
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<StructureSection load='1yk4' size='340' side='right'caption='[[1yk4]], [[Resolution|resolution]] 0.69&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'>[[1yk4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YK4 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]] 0.69&#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=FE:FE+(III)+ION'>FE</scene></td></tr>
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{{STRUCTURE_1yk4| PDB=1yk4 | 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=1yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yk4 OCA], [https://pdbe.org/1yk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yk4 RCSB], [https://www.ebi.ac.uk/pdbsum/1yk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yk4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RUBR_PYRAB RUBR_PYRAB] 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 (By similarity).
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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/yk/1yk4_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=1yk4 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 crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.
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===Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S===
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Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.,Bonisch H, Schmidt CL, Bianco P, Ladenstein R Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):990-1004. Epub 2005, Jun 24. PMID:15983423<ref>PMID:15983423</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 1yk4" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15983423}}, adds the Publication Abstract to the page
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*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15983423 is the PubMed ID number.
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*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
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*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
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{{ABSTRACT_PUBMED_15983423}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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1YK4 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YK4 OCA].
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</StructureSection>
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[[Category: Large Structures]]
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==Reference==
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<ref group="xtra">PMID:15983423</ref><references group="xtra"/>
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[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
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[[Category: Bianco, P.]]
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[[Category: Bianco P]]
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[[Category: Bonisch, H.]]
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[[Category: Bonisch H]]
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[[Category: Ladenstein, R.]]
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[[Category: Ladenstein R]]
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[[Category: Schmidt, C L.]]
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[[Category: Schmidt CL]]
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[[Category: Electron transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:20:40 2009''
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Current revision

Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S

PDB ID 1yk4

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