4GLA

OBody NL8 bound to hen egg-white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold.

Steemson, J.D.Baake, M.Rakonjac, J.Arcus, V.L.Liddament, M.T.

(2014) Plos One 9: e86050-e86050

  • DOI: 10.1371/journal.pone.0086050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class ...

    The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class of non-immunoglobulin alternatives to antibodies with unique structural and biophysical characteristics. We present here the engineering of the OB-fold anticodon recognition domain from aspartyl tRNA synthetase taken from the thermophile Pyrobaculum aerophilum. For this single-domain scaffold we have coined the term OBody. Starting from a naïve combinatorial library, we engineered an OBody with 3 nM affinity for hen egg-white lysozyme, by optimising the affinity of a naïve OBody 11,700-fold over several affinity maturation steps, using phage display. At each maturation step a crystal structure of the engineered OBody in complex with hen egg-white lysozyme was determined, showing binding elements in atomic detail. These structures have given us an unprecedented insight into the directed evolution of affinity for a single antigen on the molecular scale. The engineered OBodies retain the high thermal stability of the parental OB-fold despite mutation of up to 22% of their residues. They can be expressed in soluble form and also purified from bacteria at high yields. They also lack disulfide bonds. These data demonstrate the potential of OBodies as a new scaffold for the engineering of specific binding reagents and provide a platform for further development of future OBody-based applications.


    Organizational Affiliation

    Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.,Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.,OBodies Limited, Hamilton, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A, B
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OBody NL8
C, D
109Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)Mutation(s): 0 
Gene Names: aspS
EC: 6.1.1.12
Find proteins for Q8ZYM8 (Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827))
Go to UniProtKB:  Q8ZYM8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 76.759α = 90.00
b = 76.759β = 90.00
c = 166.344γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-14 
  • Released Date: 2013-08-14 
  • Deposition Author(s): Steemson, J.D.

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references