1XWO | pdb_00001xwo

crystal structrue of goose delta crystallin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.289 (Depositor) 
  • R-Value Work: 
    0.210 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1XWO

This is version 1.3 of the entry. See complete history

Literature

The effect of N-terminal truncation on double-dimer assembly of goose delta-crystallin

Lee, H.J.Lai, Y.H.Wu, S.Y.Chen, Y.H.

(2005) Biochem J 392: 545-554

  • DOI: https://doi.org/10.1042/BJ20050860
  • Primary Citation Related Structures: 
    1XWO

  • PubMed Abstract: 

    Delta-crystallin is a soluble structural protein in avian eye lenses that confers special refractive properties. In the presence of GdmCl (guanidinium chloride), tetrameric delta-crystallin undergoes dissociation via a dimeric state to a monomeric molten globule intermediate state. The latter are denatured at higher GdmCl concentrations in a multi-state manner. In the present study, the X-ray structure of goose delta-crystallin was determined to 2.8 A (1 A=0.1 nm). In this structure the first 25 N-terminal residues interact with a hydrophobic cavity in a neighbouring molecule, stabilizing the quaternary structure of this protein. When these 25 residues were deleted this did not produce any gross structural changes, as judged by CD analysis, but slightly altered tryptophan fluorescence and ANS (8-anilino-1-naphthalenesulphonic acid) spectra. The dimeric form was significantly identified as judged by sedimentation velocity and nondenaturing gradient gel electrophoresis. This mutant had increased sensitivity to temperature denaturation and GdmCl concentrations of 0.3-1.0 M. This protein was destabilized about 3.3 kcal/mol (1 kcal=4.184 kJ) due to N-terminal truncation. After incubation at 37 degrees C N-terminal truncated proteins were prone to aggregation, suggesting the presence of the unstable dimeric conformation. An important role for the N-terminus in dimer assembly of goose delta-crystallin is proposed.


  • Organizational Affiliation
    • Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan. hjlee@mail.ndmctsgh.edu.tw

Macromolecule Content 

  • Total Structure Weight: 205.2 kDa 
  • Atom Count: 14,142 
  • Modeled Residue Count: 1,794 
  • Deposited Residue Count: 1,860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Delta crystallin
A, B, C, D
465Anser anser anserMutation(s): 0 
EC: 4.3.2.1
UniProt
Find proteins for P33110 (Anser anser anser)
Explore P33110 
Go to UniProtKB:  P33110
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33110
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.289 (Depositor) 
  • R-Value Work:  0.210 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.7α = 90
b = 99β = 101.4
c = 106.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references