3MG5

Core-streptavidin mutant F130L in complex with biotin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

Baugh, L.Le Trong, I.Cerutti, D.S.Gulich, S.Stayton, P.S.Stenkamp, R.E.Lybrand, T.P.

(2010) Biochemistry 49: 4568-4570

  • DOI: 10.1021/bi1005392

  • PubMed Abstract: 
  • We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; howe ...

    We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B, C, D
127Streptomyces avidiniiMutation(s): 1 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 %)
BTNΔH: -66.9 - -123 kJ/mol (99) BINDINGDB
BTNKd: 1 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.910α = 90.00
b = 97.530β = 112.30
c = 52.680γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
CCP4model building
REFMACrefinement
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description