4NKM

Crystal structure of engineered anti-EE scFv antibody fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments.

Kalyoncu, S.Hyun, J.Pai, J.C.Johnson, J.L.Entzminger, K.Jain, A.Heaner, D.P.Morales, I.A.Truskett, T.M.Maynard, J.A.Lieberman, R.L.

(2014) Proteins 82: 1884-1895

  • DOI: 10.1002/prot.24542
  • Primary Citation of Related Structures:  
    4NKM, 4NKO, 4NKD

  • PubMed Abstract: 
  • Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain ...

    Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts.


    Organizational Affiliation

    School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, 30332-0400.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Engineered scFv heavy chainACEG133Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Engineered scFv light chainBDFH138Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.265α = 90
b = 92.257β = 110.86
c = 142.708γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2014-09-03
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description