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==STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTION==
==STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTION==
<StructureSection load='2scp' size='340' side='right' caption='[[2scp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='2scp' size='340' side='right'caption='[[2scp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2scp]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1scp 1scp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2SCP FirstGlance]. <br>
<table><tr><td colspan='2'>[[2scp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hediste_diversicolor Hediste diversicolor]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1scp 1scp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2SCP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2&#8491;</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=2scp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2scp OCA], [http://pdbe.org/2scp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2scp RCSB], [http://www.ebi.ac.uk/pdbsum/2scp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2scp ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2scp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2scp OCA], [https://pdbe.org/2scp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2scp RCSB], [https://www.ebi.ac.uk/pdbsum/2scp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2scp ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SCP_HEDDI SCP_HEDDI]] Like parvalbumins, SCP's seem to be more abundant in fast contracting muscles, but no functional relationship can be established from this distribution.  
[https://www.uniprot.org/uniprot/SCP_HEDDI SCP_HEDDI] Like parvalbumins, SCP's seem to be more abundant in fast contracting muscles, but no functional relationship can be established from this distribution.
== 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/sc/2scp_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sc/2scp_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=2scp 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=2scp ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of a sarcoplasmic Ca(2+)-binding protein (SCP) from the sandworm Nereis diversicolor has been determined and refined at 2.0 A resolution using restrained least-squares techniques. The two molecules in the crystallographic asymmetric unit, which are related by a non-crystallographic 2-fold axis, were refined independently. The refined model includes all 174 residues and three calcium ions for each molecule, as well as 213 water molecules. The root-mean-square difference in co-ordinates for backbone atoms and calcium ions of the two molecules is 0.51 A. The final crystallographic R-factor, based on 18,959 reflections in the range 2.0 A less than or equal to d less than or equal to 7.0 A, with intensities exceeding 2.0 sigma, is 0.182. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0.013 A and 2.2 degrees, respectively. SCP has four distinct domains with the typical helix-loop-helix (EF-hand) Ca(2+)-binding motif, although the second Ca(2+)-binding domain is not functional due to amino acid changes in the loop. The structure shows several unique features compared to other Ca(2+)-binding proteins with four EF-hand domains. The overall structure is highly compact and globular with a predominant hydrophobic core, unlike the extended dumbbell-shaped structure of calmodulin or troponin C. A hydrophobic tail at the COOH terminus adds to the structural stability by packing against a hydrophobic pocket created by the folding of the NH2 and COOH-terminal Ca(2+)-binding domain pairs. The first and second domains show different helix-packing arrangements from any previously described for Ca(2+)-binding proteins.


Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2.0 A resolution.,Vijay-Kumar S, Cook WJ J Mol Biol. 1992 Mar 20;224(2):413-26. PMID:1560459<ref>PMID:1560459</ref>
==See Also==
 
*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2scp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cook, W J]]
[[Category: Hediste diversicolor]]
[[Category: Vijay-Kumar, S]]
[[Category: Large Structures]]
[[Category: Binding protein]]
[[Category: Cook WJ]]
[[Category: Vijay-Kumar S]]

Latest revision as of 12:23, 21 February 2024

STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTIONSTRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTION

Structural highlights

2scp is a 2 chain structure with sequence from Hediste diversicolor. This structure supersedes the now removed PDB entry 1scp. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCP_HEDDI Like parvalbumins, SCP's seem to be more abundant in fast contracting muscles, but no functional relationship can be established from this distribution.

Evolutionary Conservation

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

See Also

2scp, resolution 2.00Å

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