1lil | pdb_00001lil
BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of protein Cle, a human light-chain dimer from the lambdaIII subgroup, was determined using 2.6 A data; the R value is 18.4%. The structure was solved, after a false start, by molecular replacement with the lambdaII/V Mcg protein as a search structure. When the refinement did not proceed beyond an R value of 27%, it was discovered that while the constant domains were in their correct positions in the unit cell, the incorrect variable domains were used for defining the molecule. The correct solution required a rotation of 180 degrees around the local twofold axis that relates the two constant domains of the dimer. The correct variable domain positions overlap about 70% of the same volume as the incorrect ones of a symmetry-related molecule. The refinement distorted the geometries of the domains. Though the constant domains were in their correct positions, the r.m.s. (root-mean-square) deviation of the Calpha atom position was 1.2 A when the two constant domains were compared. For the correct structure, this value is 0.5 A. The phi and psi angles, the r.m.s. chiral value and the free R value, even when calculated a posteriori, were good indicators of the correctness of the structure. The quaternary structure of the Cle molecule is similar to that in Mcg (crystallized from ammonium sulfate); the elbow bend is 115 degrees. However, the arrangement of the variable domains differs from that observed in other variable domain dimers. The variable domains of Cle are 0.7 A closer than in Mcg or variable dimer Rei. The hydrogen bonding at the interface of the two domains is novel. Residues Tyr36 from both monomers form a hydrogen bond that is part of a network with the Gln89 residues from both monomers. For the first time hydrogen bonds were observed between the main-chain peptide N and O atoms of the complementarity-determining region CDR2 and CDR3 segments of both monomers. Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer.,Huang DB, Ainsworth C, Solomon A, Schiffer M Acta Crystallogr D Biol Crystallogr. 1996 Nov 1;52(Pt 6):1058-66. PMID:15299564[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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