1LGV

Structure of a Human Bence-Jones Dimer Crystallized in U.S. Space Shuttle Mission STS-95: 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95

Terzyan, S.S.DeWitt, C.R.Ramsland, P.A.Bourne, P.C.Edmundson, A.B.

(2003) J Mol Recognit 16: 83-90

  • DOI: 10.1002/jmr.610
  • Primary Citation of Related Structures:  
    1LGV, 1LHZ

  • PubMed Abstract: 
  • Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space ...

    Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8 x 1.6 x 1.0 mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P2(1)2(1)2(1), with a = 48.9 A, b = 85.2 A, and c = 114.0 A. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293 K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues.


    Related Citations: 
    • Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties.
      BOURNE, P.C., RAMSLAND, P.A., SHAN, L., Fan, Z.C., DeWitt, C.R., SHULTZ, B.B., Terzyans, S.S., Moomaw, C.R., Slaughter, C.A., Guddat, L.W., Edmundson, A.B.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 815

    Organizational Affiliation

    Crystallography Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN LAMBDA LIGHT CHAINA, B216Homo sapiensMutation(s): 0 
Find proteins for Q6PJG0 (Homo sapiens)
Explore Q6PJG0 
Go to UniProtKB:  Q6PJG0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, BL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.339α = 90
b = 83.248β = 90
c = 112.238γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-19
    Changes: Other
  • Version 2.0: 2019-12-25
    Changes: Advisory, Derived calculations, Polymer sequence