1pij: Difference between revisions
New page: left|200px<br /><applet load="1pij" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pij" /> '''THE THREE DIMENSIONAL STRUCTURE OF THE PARAM... |
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== | ==THE THREE DIMENSIONAL STRUCTURE OF THE PARAMAGNETIC PROTEIN HIPIP I FROM E.HALOPHILA THROUGH NUCLEAR MAGNETIC RESONANCE== | ||
The three-dimensional structure in solution of reduced recombinant | <StructureSection load='1pij' size='340' side='right'caption='[[1pij]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1pij]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PIJ FirstGlance]. <br> | |||
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1pij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pij OCA], [https://pdbe.org/1pij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pij RCSB], [https://www.ebi.ac.uk/pdbsum/1pij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pij ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/HIP1_HALHA HIP1_HALHA] Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/1pij_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1pij ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The three-dimensional structure in solution of reduced recombinant high-potential iron-sulfur protein iso-I from Ectothiorhodospira halophila was determined using 948 relevant interproton NOEs out of the 1246 observed NOEs. The determination was accomplished using the XEASY program for spectral analysis and the distance geometry (DG) program DIANA for generation of the structure as described by Wuthrich [Wuthrich, K. (1989) Acc. Chem. Res. 22, 36-44]. The FeS cluster was simulated using an amino acid residue constructed for the present work from a cysteinyl residue with an iron and a sulfur atom attached to the terminal thiol. The family of structures obtained from distance geometry were subjected to energy minimization and molecular dynamics simulations using previously defined force field parameters. The quality of these structures at each stage of the refinement process is discussed with respect to the dihedral angle order parameter and the root-mean-square deviation of the atomic coordinates. The latter values for the backbone atoms vary from 67 pm for the distance-geometry structures to 60 pm for the energy-minimized structures to 51 pm for the structures subjected to restrained molecular dynamics. Finally, the structure in best agreement with the NOE constraints has been further treated with extensive restrained molecular dynamics in water. The solution structure is well defined and is very similar to the available X-ray structure. We do not know of any previous determination of the structure of a paramagnetic protein in solution by NMR. The effect of paramagnetism on the quality of the structure determination is discussed. | |||
The three-dimensional structure in solution of the paramagnetic high-potential iron-sulfur protein I from Ectothiorhodospira halophila through nuclear magnetic resonance.,Banci L, Bertini I, Eltis LD, Felli IC, Kastrau DH, Luchinat C, Piccioli M, Pierattelli R, Smith M Eur J Biochem. 1994 Oct 15;225(2):715-25. PMID:7957187<ref>PMID:7957187</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1pij" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Halorhodospira halophila]] | [[Category: Halorhodospira halophila]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Banci | [[Category: Banci L]] | ||
[[Category: Bertini | [[Category: Bertini I]] | ||
[[Category: Eltis | [[Category: Eltis LD]] | ||
[[Category: Felli | [[Category: Felli IC]] | ||
[[Category: Kastrau | [[Category: Kastrau DHW]] | ||
[[Category: Luchinat | [[Category: Luchinat C]] | ||
[[Category: Piccioli | [[Category: Piccioli M]] | ||
[[Category: Pierattelli | [[Category: Pierattelli R]] | ||
[[Category: Smith | [[Category: Smith M]] | ||
Latest revision as of 11:59, 22 May 2024
THE THREE DIMENSIONAL STRUCTURE OF THE PARAMAGNETIC PROTEIN HIPIP I FROM E.HALOPHILA THROUGH NUCLEAR MAGNETIC RESONANCETHE THREE DIMENSIONAL STRUCTURE OF THE PARAMAGNETIC PROTEIN HIPIP I FROM E.HALOPHILA THROUGH NUCLEAR MAGNETIC RESONANCE
Structural highlights
FunctionHIP1_HALHA Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe three-dimensional structure in solution of reduced recombinant high-potential iron-sulfur protein iso-I from Ectothiorhodospira halophila was determined using 948 relevant interproton NOEs out of the 1246 observed NOEs. The determination was accomplished using the XEASY program for spectral analysis and the distance geometry (DG) program DIANA for generation of the structure as described by Wuthrich [Wuthrich, K. (1989) Acc. Chem. Res. 22, 36-44]. The FeS cluster was simulated using an amino acid residue constructed for the present work from a cysteinyl residue with an iron and a sulfur atom attached to the terminal thiol. The family of structures obtained from distance geometry were subjected to energy minimization and molecular dynamics simulations using previously defined force field parameters. The quality of these structures at each stage of the refinement process is discussed with respect to the dihedral angle order parameter and the root-mean-square deviation of the atomic coordinates. The latter values for the backbone atoms vary from 67 pm for the distance-geometry structures to 60 pm for the energy-minimized structures to 51 pm for the structures subjected to restrained molecular dynamics. Finally, the structure in best agreement with the NOE constraints has been further treated with extensive restrained molecular dynamics in water. The solution structure is well defined and is very similar to the available X-ray structure. We do not know of any previous determination of the structure of a paramagnetic protein in solution by NMR. The effect of paramagnetism on the quality of the structure determination is discussed. The three-dimensional structure in solution of the paramagnetic high-potential iron-sulfur protein I from Ectothiorhodospira halophila through nuclear magnetic resonance.,Banci L, Bertini I, Eltis LD, Felli IC, Kastrau DH, Luchinat C, Piccioli M, Pierattelli R, Smith M Eur J Biochem. 1994 Oct 15;225(2):715-25. PMID:7957187[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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