1AYP

A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT

Summary for 1AYP

• Entry DOI: 10.2210/pdb1ayp/pdb
• Descriptor: PHOSPHOLIPASE A2, CALCIUM ION, 1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE, ... (4 entities in total)
• Functional Keywords: hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Membrane; Peripheral membrane protein: P14555
• Total number of polymer chains: 6
• Total formula weight: 87389.50

Authors

Oh, B.-H. (deposition date: 1994-07-19, release date: 1995-07-31, Last modification date: 2024-10-16)

Primary citation

Oh, B.H.
A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement.
Acta Crystallogr.,Sect.D, 51:140-144, 1995

PubMed Abstract: It is often found in the crystallization of enzyme-inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A(2) (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method.

PubMed: 15299314
DOI: 10.1107/S0907444994010024

Experimental method

X-RAY DIFFRACTION (2.57 Å)