2blv: Difference between revisions
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==Overview== | ==Overview== | ||
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, ... | 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 Structure== | ==About this Structure== | ||
2BLV is a | 2BLV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA, SO4, BEN and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BLV OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: zymogen]] | [[Category: zymogen]] | ||
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Revision as of 15:56, 5 November 2007
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TRYPSIN BEFORE 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
2BLV is a Single protein structure of sequence from Bos taurus with CA, SO4, BEN and GOL as ligands. Active as Trypsin, with EC number 3.4.21.4 Structure known Active Site: AC1. 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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