2BN3

Insulin before a high dose x-ray burn

Summary for 2BN3

• Entry DOI: 10.2210/pdb2bn3/pdb
• Related: 1B17 1B18 1B19 1B2A 1B2B 1B2C 1B2D 1B2E 1B2F 1B2G 1DEI 1IZA 1IZB 1M5A 1MPJ 1SDB 1WAV 1ZEI 1ZNI 2TCI 3INS 3MTH 4INS 6INS 7INS 9INS
• Descriptor: INSULIN (3 entities in total)
• Functional Keywords: radiation damage, synchrotron, phasing, rip, carbohydrate metabolism, glucose metabolism, hormone, insulin family
• Biological source: BOS TAURUS (BOVINE); More
• Cellular location: Secreted: P01317 P01317
• Total number of polymer chains: 2
• Total formula weight: 5773.60

Authors

Nanao, M.H.,Ravelli, R.B. (deposition date: 2005-03-18, release date: 2005-09-07, Last modification date: 2024-11-13)

Primary citation

Nanao, M.H.,Sheldrick, G.M.,Ravelli, R.B.
Improving Radiation-Damage Substructures for Rip.
Acta Crystallogr.,Sect.D, 61:1227-, 2005

PubMed Abstract: 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.

PubMed: 16131756
DOI: 10.1107/S0907444905019360

Experimental method

X-RAY DIFFRACTION (1.4 Å)