2fd9: Difference between revisions

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[[Image:2fd9.png|left|200px]]


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==X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide==
The line below this paragraph, containing "STRUCTURE_2fd9", creates the "Structure Box" on the page.
<StructureSection load='2fd9' size='340' side='right'caption='[[2fd9]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2fd9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crambe_hispanica_subsp._abyssinica Crambe hispanica subsp. abyssinica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FD9 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fd9 OCA], [https://pdbe.org/2fd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fd9 RCSB], [https://www.ebi.ac.uk/pdbsum/2fd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fd9 ProSAT]</span></td></tr>
{{STRUCTURE_2fd9|  PDB=2fd9  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/CRAM_CRAAB CRAM_CRAAB] The function of this hydrophobic plant seed protein 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/fd/2fd9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2fd9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have used total chemical synthesis to prepare [V15A]crambin-alpha-carboxamide, a unique protein analogue that eliminates a salt bridge between the delta-guanidinium of the Arg(10) side chain and the alpha-carboxylate of Asn(46) at the C-terminus of the polypeptide chain. This salt bridge is thought to be important for the folding and stability of the crambin protein molecule. Folding, with concomitant disulfide bond formation, of the fully reduced [V15A]crambin-alpha-carboxamide polypeptide was less efficient than folding/disulfide formation for the [V15A]crambin polypeptide under a standard set of conditions. To probe the origin of this less efficient folding/disulfide bond formation, we separately crystallized purified synthetic [V15A]crambin-alpha-carboxamide and chemically synthesized [V15A]crambin and solved their X-ray structures. The crystal structure of [V15A]crambin-alpha-carboxamide showed that elimination of the Arg(10)-Asn(46) salt bridge caused disorder of the C-terminal region of the polypeptide chain and affected the overall 'tightness' of the structure of the protein molecule. These studies, enabled by chemical protein synthesis, strongly suggest that in native crambin the Arg(10)-Asn(46) salt bridge contributes to efficient formation of correct disulfide bonds and also to the well-ordered structure of the protein molecule.


===X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide===
Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide.,Bang D, Tereshko V, Kossiakoff AA, Kent SB Mol Biosyst. 2009 Jul;5(7):750-6. Epub 2009 May 28. PMID:19562114<ref>PMID:19562114</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_19562114}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2fd9" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19562114 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19562114}}
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</StructureSection>
==About this Structure==
[[Category: Crambe hispanica subsp. abyssinica]]
[[2fd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FD9 OCA].
[[Category: Large Structures]]
 
[[Category: Bang D]]
==Reference==
[[Category: Kent SB]]
<ref group="xtra">PMID:19562114</ref><references group="xtra"/>
[[Category: Kossiakoff AA]]
[[Category: Bang, D.]]
[[Category: Tereshko V]]
[[Category: Kent, S B.]]
[[Category: Kossiakoff, A A.]]
[[Category: Tereshko, V.]]

Latest revision as of 10:59, 30 October 2024

X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide

Structural highlights

2fd9 is a 1 chain structure with sequence from Crambe hispanica subsp. abyssinica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CRAM_CRAAB The function of this hydrophobic plant seed protein 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 PubMed

We have used total chemical synthesis to prepare [V15A]crambin-alpha-carboxamide, a unique protein analogue that eliminates a salt bridge between the delta-guanidinium of the Arg(10) side chain and the alpha-carboxylate of Asn(46) at the C-terminus of the polypeptide chain. This salt bridge is thought to be important for the folding and stability of the crambin protein molecule. Folding, with concomitant disulfide bond formation, of the fully reduced [V15A]crambin-alpha-carboxamide polypeptide was less efficient than folding/disulfide formation for the [V15A]crambin polypeptide under a standard set of conditions. To probe the origin of this less efficient folding/disulfide bond formation, we separately crystallized purified synthetic [V15A]crambin-alpha-carboxamide and chemically synthesized [V15A]crambin and solved their X-ray structures. The crystal structure of [V15A]crambin-alpha-carboxamide showed that elimination of the Arg(10)-Asn(46) salt bridge caused disorder of the C-terminal region of the polypeptide chain and affected the overall 'tightness' of the structure of the protein molecule. These studies, enabled by chemical protein synthesis, strongly suggest that in native crambin the Arg(10)-Asn(46) salt bridge contributes to efficient formation of correct disulfide bonds and also to the well-ordered structure of the protein molecule.

Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide.,Bang D, Tereshko V, Kossiakoff AA, Kent SB Mol Biosyst. 2009 Jul;5(7):750-6. Epub 2009 May 28. PMID:19562114[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Bang D, Tereshko V, Kossiakoff AA, Kent SB. Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide. Mol Biosyst. 2009 Jul;5(7):750-6. Epub 2009 May 28. PMID:19562114 doi:10.1039/b903610e

2fd9, resolution 1.60Å

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