5EWX

Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.

Jeong, W.H.Lee, H.Song, D.H.Eom, J.H.Kim, S.C.Lee, H.S.Lee, H.Lee, J.O.

(2016) Nat Commun 7: 11031-11031

  • DOI: https://doi.org/10.1038/ncomms11031
  • Primary Citation of Related Structures:  
    5CBN, 5CBO, 5COC, 5EWX

  • PubMed Abstract: 

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a 'fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures.


  • Organizational Affiliation

    Department of Chemistry, KAIST, Daejeon 34141, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin,Immunoglobulin G-binding protein A,Endolysin
A, B
227Tequatrovirus T4Staphylococcus aureusMutation(s): 9 
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P38507 (Staphylococcus aureus)
Explore P38507 
Go to UniProtKB:  P38507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP38507P00720
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EYC
Query on EYC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid}
C18 H14 Cl2 N2 O8 S2
KKVZAHKPXRPKDH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.522α = 90
b = 149.85β = 122.69
c = 55.836γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description