2BLO

Elastase before a high dose x-ray "burn"

Summary for 2BLO

• Entry DOI: 10.2210/pdb2blo/pdb
• Related: 1B0E 1BMA 1BTU 1C1M 1E34 1E35 1E36 1E37 1E38 1EAI 1EAS 1EAT 1EAU 1ELA 1ELB 1ELC 1ELD 1ELE 1ELF 1ELG 1ESA 1ESB 1EST 1FLE 1FZZ 1GVK 1GWA 1H9L 1HAX 1HAY 1HAZ 1HB0 1HV7 1INC 1JIM 1L0Z 1L1G 1LKA 1LKB 1LVY 1MCV 1MMJ 1NES 1OKX 1QGF 1QIX 1QNJ 1QR3 1UO6 1UVO 1UVP 2BLO 2EST 3EST 4EST 5EST 6EST 7EST 8EST 9EST
• Descriptor: ELASTASE 1, CALCIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: radiation damage, synchrotron, phasing, rip, hydrolase
• Biological source: SUS SCROFA (PIG)
• Cellular location: Secreted: P00772
• Total number of polymer chains: 1
• Total formula weight: 26161.22

Authors

Nanao, M.H.,Ravelli, R.B. (deposition date: 2005-03-08, release date: 2005-09-07, Last modification date: 2024-10-23)

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 (1.33 Å)