1LIL

BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer.

Huang, D.B.Ainsworth, C.Solomon, A.Schiffer, M.

(1996) Acta Crystallogr D Biol Crystallogr 52: 1058-1066

  • DOI: 10.1107/S090744499600813X
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The 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 s ...

    The 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.


    Related Citations: 
    • Preliminary Crystallographic Data on the Human Lambda III Bence Jones Protein Dimer Cle
      Stevens, F.J., Westholm, F.A., Panagiotopoulos, N., Solomon, A., Schiffer, M.
      (1981) J Mol Biol 147: 179

    Organizational Affiliation

    Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, Illinois 60439-4833, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LAMBDA III BENCE JONES PROTEIN CLE
A, B
212Homo sapiensMutation(s): 0 
Gene Names: IGLC2
Find proteins for P0DOY2 (Homo sapiens)
Go to UniProtKB:  P0DOY2
NIH Common Fund Data Resources
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.17α = 90
b = 72.54β = 90
c = 49.25γ = 90
Software Package:
Software NamePurpose
LARRYdata collection
SCALINGdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
LARRYdata reduction
SCALINGdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance