4ekb: Difference between revisions

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[[Image:4ekb.png|left|200px]]
==Initial Thaumatin Structure for Radiation Damage Experiment at 100 K==
<StructureSection load='4ekb' size='340' side='right' caption='[[4ekb]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4ekb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EKB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ek0|4ek0]], [[4eka|4eka]], [[4ekh|4ekh]], [[4eko|4eko]], [[4ekt|4ekt]], [[4el2|4el2]], [[4el3|4el3]], [[4el7|4el7]], [[4ela|4ela]]</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=4ekb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ekb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ekb RCSB], [http://www.ebi.ac.uk/pdbsum/4ekb PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/THM1_THADA THM1_THADA]] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.


{{STRUCTURE_4ekb|  PDB=4ekb  |  SCENE=  }}
Spatial distribution of radiation damage to crystalline proteins at 25-300 K.,Warkentin M, Badeau R, Hopkins JB, Thorne RE Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1108-17. doi:, 10.1107/S0907444912021361. Epub 2012 Aug 18. PMID:22948911<ref>PMID:22948911</ref>


===Initial Thaumatin Structure for Radiation Damage Experiment at 100 K===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_22948911}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[4ekb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EKB OCA].
</StructureSection>
[[Category: Thaumatococcus daniellii]]
[[Category: Thaumatococcus daniellii]]
[[Category: Badeau, R.]]
[[Category: Badeau, R]]
[[Category: Hopkins, J B.]]
[[Category: Hopkins, J B]]
[[Category: Thorne, R E.]]
[[Category: Thorne, R E]]
[[Category: Warkentin, M.]]
[[Category: Warkentin, M]]
[[Category: Plant protein]]
[[Category: Plant protein]]
[[Category: Radiation damage]]
[[Category: Radiation damage]]
[[Category: Sweet protein]]
[[Category: Sweet protein]]

Revision as of 07:26, 25 December 2014

Initial Thaumatin Structure for Radiation Damage Experiment at 100 KInitial Thaumatin Structure for Radiation Damage Experiment at 100 K

Structural highlights

4ekb is a 1 chain structure with sequence from Thaumatococcus daniellii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, RCSB, PDBsum

Function

[THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.

Publication Abstract from PubMed

The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.

Spatial distribution of radiation damage to crystalline proteins at 25-300 K.,Warkentin M, Badeau R, Hopkins JB, Thorne RE Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1108-17. doi:, 10.1107/S0907444912021361. Epub 2012 Aug 18. PMID:22948911[1]

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

References

  1. Warkentin M, Badeau R, Hopkins JB, Thorne RE. Spatial distribution of radiation damage to crystalline proteins at 25-300 K. Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1108-17. doi:, 10.1107/S0907444912021361. Epub 2012 Aug 18. PMID:22948911 doi:http://dx.doi.org/10.1107/S0907444912021361

4ekb, resolution 1.52Å

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