2pya
From Proteopedia
(Difference between revisions)
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<StructureSection load='2pya' size='340' side='right'caption='[[2pya]], [[Resolution|resolution]] 0.86Å' scene=''> | <StructureSection load='2pya' size='340' side='right'caption='[[2pya]], [[Resolution|resolution]] 0.86Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2pya]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[2pya]] 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=2PYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYA FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.86Å</td></tr> |
| - | <tr id=' | + | <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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
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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=2pya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pya OCA], [https://pdbe.org/2pya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pya RCSB], [https://www.ebi.ac.uk/pdbsum/2pya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pya ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pya OCA], [https://pdbe.org/2pya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pya RCSB], [https://www.ebi.ac.uk/pdbsum/2pya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pya ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [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). | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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=2pya ConSurf]. | </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=2pya ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The effect of D-H...S(gamma)-Fe hydrogen bonding on the reduction potential of rubredoxin was investigated by the introduction of an O-H...S(gamma)-Fe hydrogen bond on the surface of Pyrococcus abyssi rubredoxin. The formation of a weak hydrogen bond between Ser44-O(gamma) and Cys42-S(gamma) in mutant W4L/R5S/A44S increased the reduction potential by 56 mV. When side effects of the mutation were taken into account, the contribution of the additional cluster hydrogen bond to the reduction potential was estimated to be +65 mV. The structural analysis was based on ultrahigh-resolution structures of oxidized P. abyssi rubredoxin W4L/R5S and W4L/R5S/A44S refined to 0.69 and 0.86 A, respectively. | ||
| - | + | ==See Also== | |
| - | + | *[[Rubredoxin 3D structures|Rubredoxin 3D structures]] | |
| - | + | *[[Rubredoxin PDB structures|Rubredoxin PDB structures]] | |
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: | + | [[Category: Boenisch H]] |
| - | [[Category: | + | [[Category: Ladenstein R]] |
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Current revision
Ultra-high resolution structure of P. abyssi rubredoxin W4L/R5S/A44S
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