1SWR

CORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN AT PH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex.

Freitag, S.Le Trong, I.Chilkoti, A.Klumb, L.A.Stayton, P.S.Stenkamp, R.E.

(1998) J Mol Biol 279: 211-221

  • DOI: 10.1006/jmbi.1998.1735
  • Primary Citation of Related Structures:  
    1SWL, 1SWK, 1SWJ, 1SWH, 1SWR, 1SWQ, 1SWP, 1SWO, 1SWN

  • PubMed Abstract: 
  • Previous thermodynamic and computational studies have pointed to the important energetic role of aromatic contacts in generating the exceptional binding free energy of streptavidin-biotin association. We report here the crystallographic characterizat ...

    Previous thermodynamic and computational studies have pointed to the important energetic role of aromatic contacts in generating the exceptional binding free energy of streptavidin-biotin association. We report here the crystallographic characterization of single site tryptophan mutants in investigating structural consequences of alterations in these aromatic contacts. Four tryptophan residues, Trp79, Trp92, Trp108 and Trp120, play an important role in the hydrophobic binding contributions, which along with a hydrogen bonding network and a flexible binding loop give rise to tight ligand binding (Ka approximately 10(13) M-1). The crystal structures of ligand-free and biotin-bound mutants, W79F, W108F, W120F and W120A, in the resolution range from 1.9 to 2.3 A were determined. Nine data sets for these four different mutants were collected, and structural models were refined to R-values ranging from 0.15 to 0.20. The major question addressed here is how these mutations influence the streptavidin binding site and in particular how they affect the binding mode of biotin in the complex. The overall folding of streptavidin was not significantly altered in any of the tryptophan mutants. With one exception, only minor deviations in the unbound structures were observed. In one crystal form of unbound W79F, there is a coupled shift in the side-chains of Phe29 and Tyr43 toward the mutation site, although in a different crystal form these shifts are not observed. In the bound structures, the orientation of biotin in the binding pocket was not significantly altered in the mutant complex. Compared with the wild-type streptavidin-biotin complex, there were no additional crystallographic water molecules observed for any of the mutants in the binding pocket. These structural studies thus suggest that the thermodynamic alterations can be attributed to the local alterations in binding residue composition, rather than a rearrangement of binding site architectures.


    Related Citations: 
    • 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
    • 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

    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195-7420, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CORE-STREPTAVIDINA, B, C, D127Streptomyces avidiniiMutation(s): 1 
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

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:  107.52999877929688   kJ/mol  BindingDB
BTNKd:  120   nM  Binding MOAD
BTNKd :  120   nM  PDBBind
BTNΔH:  100.41999816894531   kJ/mol  BindingDB
BTNΔH:  66.94000244140625   kJ/mol  BindingDB
BTNΔH:  123.01000213623047   kJ/mol  BindingDB
BTNΔH:  102.51000213623047   kJ/mol  BindingDB
BTNKd:  1   nM  BindingDB
BTNΔH:  117.98999786376953   kJ/mol  BindingDB
BTNΔH:  104.18000030517578   kJ/mol  BindingDB
BTNΔH:  97.48999786376953   kJ/mol  BindingDB
BTNΔH:  115.05999755859375   kJ/mol  BindingDB
BTNΔH:  90.37000274658203   kJ/mol  BindingDB
BTNΔH:  89.95999908447266   kJ/mol  BindingDB
BTNΔH:  75.30999755859375   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.8α = 90
b = 99.9β = 112.7
c = 50.9γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance