1eky: Difference between revisions
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< | ==MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION== | ||
<StructureSection load='1eky' size='340' side='right'caption='[[1eky]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1eky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKY 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1eky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eky OCA], [https://pdbe.org/1eky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eky RCSB], [https://www.ebi.ac.uk/pdbsum/1eky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eky ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CYCP_RHOCA CYCP_RHOCA] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known. | |||
== 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/ek/1eky_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=1eky ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation. | |||
De novo determination of protein structure by NMR using orientational and long-range order restraints.,Hus JC, Marion D, Blackledge M J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359<ref>PMID:10801359</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1eky" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
< | |||
[[Category: Rhodobacter capsulatus]] | [[Category: Rhodobacter capsulatus]] | ||
[[Category: Blackledge | [[Category: Blackledge M]] | ||
[[Category: Hus | [[Category: Hus JC]] | ||
[[Category: Marion | [[Category: Marion D]] | ||
Latest revision as of 11:26, 22 May 2024
MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATIONMODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION
Structural highlights
FunctionCYCP_RHOCA Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known. 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 PubMedOrientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation. De novo determination of protein structure by NMR using orientational and long-range order restraints.,Hus JC, Marion D, Blackledge M J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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