1SWG

CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

Chu, V.Freitag, S.Le Trong, I.Stenkamp, R.E.Stayton, P.S.

(1998) Protein Sci. 7: 848-859

  • DOI: 10.1002/pro.5560070403
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and fo ...

    A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin.


    Related Citations: 
    • Structural Studies of the Streptavidin Binding Loop
      Freitag, S.,Le Trong, I.,Klumb, L.,Stayton, P.S.,Stenkamp, R.E.
      (1997) Protein Sci. 6: 1157
    • Thermodynamic Consequences of the Deletion of a Flexible Loop by Circular Permutation in the Streptavidin-Biotin System
      Chu, V.,Freitag, S.,Le Trong, I.,Stenkamp, R.E.,Stayton, P.S.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Bioengineering, University of Washington, Seattle 98195-7962, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
A, B, C, D
128Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, B, C, D
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd: 1 nM (92) BINDINGDB
BTNΔH: -66.9 - -123 kJ/mol (92) BINDINGDB
BTNKd: 43.9 nM BINDINGMOAD
BTNKd: 43.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.900α = 90.00
b = 78.600β = 90.00
c = 90.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97model building
SCALEPACKdata scaling
SHELXL-97phasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance