3MCG

THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms.

Ely, K.R.Herron, J.N.Harker, M.Edmundson, A.B.

(1989) J Mol Biol 210: 601-615

  • DOI: https://doi.org/10.1016/0022-2836(89)90135-6
  • Primary Citation of Related Structures:  
    1DCL, 2MCG, 3MCG

  • PubMed Abstract: 

    The three-dimensional structure of an immunoglobulin light chain dimer (Mcg) crystallized in deionized water (orthorhombic form) was determined at 2.0 A resolution by phase extension and crystallographic refinement. This structure was refined side-by-side with that of the same molecule crystallized in ammonium sulfate (trigonal form). The dimer adopted markedly different structures in the two solvents. "Elbow bend" angles between pseudo 2-fold axes of rotation relating pairs of "variable" (V) and "constant" (C) domains were found to be 132 degrees in the orthorhombic form and 115 degrees in the trigonal form. Modes of association of the V domains and, to a lesser extent, the pairing interactions of the C domains were different in the two structures. Alterations in the V domain pairing were reflected in the shapes of the binding regions and in the orientations of the side-chains lining the walls of the binding sites. In the trigonal form, for instance, the V domain interface was compartmentalized into a main binding cavity and a deep pocket, whereas these spaces were continuous in the orthorhombic structure. Patterns of ordered water molecules were quite distinct in the two crystal types. In some cases, the solvent structures could be correlated with conformational changes in the proteins. For example, close contacts between V and C domains of monomer 1 of the trigonal form were not retained in orthorhombic crystals. Ordered water molecules filled the space created when the two domains moved apart.


  • Organizational Affiliation

    Department of Biology, University of Utah, Salt Lake City 84112.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)A [auth 1],
B [auth 2]
216Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01709 (Homo sapiens)
Explore P01709 
Go to UniProtKB:  P01709
GTEx:  ENSG00000278196 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01709
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth 1],
B [auth 2]
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.8α = 90
b = 81.9β = 90
c = 71γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Other, Polymer sequence