1fhh: Difference between revisions

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<StructureSection load='1fhh' size='340' side='right'caption='[[1fhh]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='1fhh' size='340' side='right'caption='[[1fhh]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1fhh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pasteurianus"_(winogradsky_1895)_lehmann_and_neumann_1907 "bacillus pasteurianus" (winogradsky 1895) lehmann and neumann 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FHH FirstGlance]. <br>
<table><tr><td colspan='2'>[[1fhh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FHH FirstGlance]. <br>
</td></tr><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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fhm|1fhm]]</div></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fhh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhh OCA], [https://pdbe.org/1fhh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fhh RCSB], [https://www.ebi.ac.uk/pdbsum/1fhh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhh 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=1fhh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhh OCA], [https://pdbe.org/1fhh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fhh RCSB], [https://www.ebi.ac.uk/pdbsum/1fhh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RUBR_CLOPA RUBR_CLOPA]] 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.  
[https://www.uniprot.org/uniprot/RUBR_CLOPA RUBR_CLOPA] 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.
== 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=1fhh 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=1fhh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Biological electron transfer is an efficient process even though the distances between the redox moieties are often quite large. It is therefore of great interest to gain an understanding of the physical basis of the rates and driving forces of these reactions. The structural relaxation of the protein that occurs upon change in redox state gives rise to the reorganizational energy, which is important in the rates and the driving forces of the proteins involved. To determine the structural relaxation in a redox protein, we have developed methods to hold a redox protein in its final oxidation state during crystallization while maintaining the same pH and salt conditions of the crystallization of the protein in its initial oxidation state. Based on 1.5 A resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated. First, expansion of the [Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to greater electrostatic stabilization of the extra negative charge. Second, a gating mechanism caused by the conformational change of Leucine 41, a nonpolar side chain, allows transient penetration of water molecules, which greatly increases the polarity of the redox site environment and also provides a source of protons. Our method of producing crystals of Cp Rd from a reducing solution leads to a distribution of water molecules not observed in the crystal structure of the reduced Rd from Pyrococcus furiosus. How general this correlation is among redox proteins must be determined in future work. The combination of our high-resolution crystal structures and molecular dynamics simulations provides a molecular picture of the structural rearrangement that occurs upon reduction in Cp rubredoxin.


Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin.,Min T, Ergenekan CE, Eidsness MK, Ichiye T, Kang C Protein Sci. 2001 Mar;10(3):613-21. PMID:11344329<ref>PMID:11344329</ref>
==See Also==
 
*[[Rubredoxin 3D structures|Rubredoxin 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
*[[Rubredoxin PDB structures|Rubredoxin PDB structures]]
</div>
<div class="pdbe-citations 1fhh" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Clostridium pasteurianum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Eidsness, M K]]
[[Category: Eidsness MK]]
[[Category: Ergenekan, C E]]
[[Category: Ergenekan CE]]
[[Category: Ichiye, T]]
[[Category: Ichiye T]]
[[Category: Kang, C]]
[[Category: Kang C]]
[[Category: Min, T]]
[[Category: Min T]]
[[Category: Cp rd]]
[[Category: Electron transport]]
[[Category: Oxidized]]
[[Category: Rubredoxin]]

Latest revision as of 10:14, 7 February 2024

X-RAY CRYSTAL STRUCTURE OF OXIDIZED RUBREDOXINX-RAY CRYSTAL STRUCTURE OF OXIDIZED RUBREDOXIN

Structural highlights

1fhh is a 1 chain structure with sequence from Clostridium pasteurianum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUBR_CLOPA 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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1fhh, resolution 1.50Å

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