2blu: Difference between revisions
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[[Image:2blu.gif|left|200px]] | [[Image:2blu.gif|left|200px]] | ||
'''THAUMATIN AFTER A HIGH DOSE X-RAY "BURN"''' | {{Structure | ||
|PDB= 2blu |SIZE=350|CAPTION= <scene name='initialview01'>2blu</scene>, resolution 1.40Å | |||
|SITE= <scene name='pdbsite=AC1:Tla+Binding+Site+For+Chain+A'>AC1</scene> | |||
|LIGAND= <scene name='pdbligand=TLA:L(+)-TARTARIC ACID'>TLA</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''THAUMATIN AFTER A HIGH DOSE X-RAY "BURN"''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2BLU is a [ | 2BLU is a [[Single protein]] structure of 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=2BLU OCA]. | ||
==Reference== | ==Reference== | ||
Improving radiation-damage substructures for RIP., Nanao MH, Sheldrick GM, Ravelli RB, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:[http:// | Improving radiation-damage substructures for RIP., Nanao MH, Sheldrick GM, Ravelli RB, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16131756 16131756] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Thaumatococcus daniellii]] | [[Category: Thaumatococcus daniellii]] | ||
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[[Category: taste-modifying protein]] | [[Category: taste-modifying protein]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:03:38 2008'' | ||
Revision as of 17:03, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
THAUMATIN AFTER A HIGH DOSE X-RAY "BURN"
OverviewOverview
Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
About this StructureAbout this Structure
2BLU is a Single protein structure of sequence from Thaumatococcus daniellii. Full crystallographic information is available from OCA.
ReferenceReference
Improving radiation-damage substructures for RIP., Nanao MH, Sheldrick GM, Ravelli RB, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:16131756
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