2BLZ

RNAse after a high dose X-ray "burn"

Summary for 2BLZ

• Entry DOI: 10.2210/pdb2blz/pdb
• Related: 1A2W 1A5P 1A5Q 1AFK 1AFL 1AFU 1AQP 1B6V 1BEL 1BZQ 1C0B 1C0C 1C8W 1C9V 1C9X 1CJQ 1CJR 1D5D 1D5E 1D5H 1DFJ 1DY5 1EIC 1EID 1EIE 1EOS 1EOW 1F0V 1FEV 1FS3 1GV7 1IZP 1IZQ 1IZR 1J7Z 1J80 1J81 1J82 1JN4 1JS0 1JVT 1JVU 1JVV 1KF2 1KF3 1KF4 1KF5 1KF7 1KF8 1KH8 1LSQ 1O0F 1O0H 1O0M 1O0N 1O0O 1QHC 1RAR 1RAS 1RAT 1RBB 1RBC 1RBD 1RBE 1RBF 1RBG 1RBH 1RBI 1RBJ 1RBN 1RBW 1RBX 1RCA 1RCN 1RHA 1RHB 1RNC 1RND 1RNM 1RNN 1RNO 1RNQ 1RNU 1RNV 1RNW 1RNX 1RNY 1RNZ 1ROB 1RPF 1RPG 1RPH 1RSM 1RTA 1RTB 1RUV 1SRN 1SSA 1SSB 1SSC 1UN5 1W4O 1W4P 1W4Q 1WBU 1XPS 1XPT 2AAS 2BLP 2RAT 2RLN 2RNS 3RAT 3RN3 3RSD 3RSK 3RSP 3SRN 4RAT 4RSD 4RSK 4SRN 5RAT 5RSA 6RAT 6RSA 7RAT 7RSA 8RAT 8RSA 9RAT 9RSA
• Descriptor: RIBONUCLEASE PANCREATIC, CHLORIDE ION (3 entities in total)
• Functional Keywords: radiation damage, synchrotron, phasing, rip, hydrolase, endonuclease, glycoprotein, nuclease
• Biological source: BOS TAURUS (BOVINE)
• Cellular location: Secreted: P61823
• Total number of polymer chains: 1
• Total formula weight: 13743.78

Authors

Nanao, M.H.,Ravelli, R.B. (deposition date: 2005-03-08, release date: 2005-09-07, Last modification date: 2011-07-13)

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)