4GLV

OBody AM3L09 bound to hen egg-white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.574 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  4GLA, 4GN3, 4GN4, 4GN5

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A, C, E, G
129Gallus gallusGene 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 AM3L09
B, D, F, H
107N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
C
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, F, G, H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.574 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.000α = 72.17
b = 69.380β = 69.46
c = 76.360γ = 77.55
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-15 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Steemson, J.D.

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Experimental preparation
  • Version 1.2: 2014-02-12
    Type: Database references