3KCH

Baranase crosslinked by glutaraldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Revisiting glutaraldehyde cross-linking: the case of the Arg-Lys intermolecular doublet

Salem, M.Mauguen, Y.Prange, T.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 225-228

  • DOI: https://doi.org/10.1107/S1744309109054037
  • Primary Citation of Related Structures:  
    3KCH

  • PubMed Abstract: 

    In addition to the common use of glutaraldehyde to nonspecifically cross-link protein crystals through lysine residues disposed on the surface of the protein, the use of gentle vapour diffusion of glutaraldehyde offers a convenient way to limit polymerization and to allow slow diffusion throughout the crystal. In the case of trimeric barnase crystals, a specific cross-link was observed between an lysine side chain and an arginine side chain that were spatially disposed at the ideal distance on the protein surface in the three monomers. Here, the direct observation of a specific Lys-Arg cross-link site is reported and a mechanism is proposed for the reaction.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques (UMR 8015 CNRS), Faculté de Pharmacie, Université Descartes, 4 Avenue de l'Observatoire, 75006 Paris, France. michele.salem@parisdescartes.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease
A, B, C
110Bacillus amyloliquefaciensMutation(s): 0 
EC: 3.1.27
UniProt
Find proteins for P00648 (Bacillus amyloliquefaciens)
Explore P00648 
Go to UniProtKB:  P00648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00648
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.97α = 90
b = 58.97β = 90
c = 82.14γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description