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==SOLUTION-STATE STRUCTURE BY NMR OF ZINC-SUBSTITUTED RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS==
==SOLUTION-STATE STRUCTURE BY NMR OF ZINC-SUBSTITUTED RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS==
<StructureSection load='1zrp' size='340' side='right' caption='[[1zrp]], [[NMR_Ensembles_of_Models | 40 NMR models]]' scene=''>
<StructureSection load='1zrp' size='340' side='right'caption='[[1zrp]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1zrp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZRP FirstGlance]. <br>
<table><tr><td colspan='2'>[[1zrp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZRP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrp OCA], [http://pdbe.org/1zrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zrp RCSB], [http://www.ebi.ac.uk/pdbsum/1zrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrp ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1zrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrp OCA], [https://pdbe.org/1zrp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zrp RCSB], [https://www.ebi.ac.uk/pdbsum/1zrp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrp ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zr/1zrp_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zr/1zrp_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 20:
</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=1zrp 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=1zrp ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. Structures were generated with DSPACE by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (NOE)-derived interproton distance restraints, including 67 interresidue, 124 sequential (i-j = 1), 75 medium-range (i-j = 2-5), and 137 long-range (i-j &gt; 5) restraints. All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backbone-side chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to &gt; 16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridium pasteurianum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +/- standard deviation) of 0.024 +/- 0.003 A2 and a maximum total penalty of 0.035 A2. Superposition of the backbone atoms (C, C alpha, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (+/- SD) of 0.42 +/- 0.07 A. Superposition of all heavy atoms for residues A1-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 +/- 0.08 A. Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pasteurianum, with the average rms deviation value for backbone atoms of residues A1-L51 of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pasteurianum Rd of 0.77 +/- 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS)


Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.,Blake PR, Park JB, Zhou ZH, Hare DR, Adams MW, Summers MF Protein Sci. 1992 Nov;1(11):1508-21. PMID:1303769<ref>PMID:1303769</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 1zrp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43587]]
[[Category: Large Structures]]
[[Category: Adams, M W.W]]
[[Category: Pyrococcus furiosus]]
[[Category: Blake, P R]]
[[Category: Adams MWW]]
[[Category: Hare, D R]]
[[Category: Blake PR]]
[[Category: Park, J B]]
[[Category: Hare DR]]
[[Category: Summers, M F]]
[[Category: Park JB]]
[[Category: Zhou, Z H]]
[[Category: Summers MF]]
[[Category: Electron transport]]
[[Category: Zhou ZH]]

Latest revision as of 09:37, 1 May 2024

SOLUTION-STATE STRUCTURE BY NMR OF ZINC-SUBSTITUTED RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUSSOLUTION-STATE STRUCTURE BY NMR OF ZINC-SUBSTITUTED RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS

Structural highlights

1zrp is a 1 chain structure with sequence from Pyrococcus furiosus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Evolutionary Conservation

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

See Also

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