1MK5

Wildtype Core-Streptavidin with Biotin at 1.4A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.189 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cooperative hydrogen bond interactions in the streptavidin-biotin system

Hyre, D.E.Le Trong, I.Merritt, E.A.Eccleston, J.F.Green, N.M.Stenkamp, R.E.Stayton, P.S.

(2006) Protein Sci 15: 459-467

  • DOI: 10.1110/ps.051970306
  • Primary Citation of Related Structures:  
    1MK5, 1MEP

  • PubMed Abstract: 
  • The thermodynamic and structural cooperativity between the Ser45- and D128-biotin hydrogen bonds was measured by calorimetric and X-ray crystallographic studies of the S45A/D128A double mutant of streptavidin. The double mutant exhibits a binding affinity approximately 2x10(7) times lower than that of wild-type streptavidin at 25 degrees C ...

    The thermodynamic and structural cooperativity between the Ser45- and D128-biotin hydrogen bonds was measured by calorimetric and X-ray crystallographic studies of the S45A/D128A double mutant of streptavidin. The double mutant exhibits a binding affinity approximately 2x10(7) times lower than that of wild-type streptavidin at 25 degrees C. The corresponding reduction in binding free energy (DeltaDeltaG) of 10.1 kcal/mol was nearly completely due to binding enthalpy losses at this temperature. The loss of binding affinity is 11-fold greater than that predicted by a linear combination of the single-mutant energetic perturbations (8.7 kcal/mol), indicating that these two mutations interact cooperatively. Crystallographic characterization of the double mutant and comparison with the two single mutant structures suggest that structural rearrangements at the S45 position, when the D128 carboxylate is removed, mask the true energetic contribution of the D128-biotin interaction. Taken together, the thermodynamic and structural analyses support the conclusion that the wild-type hydrogen bond between D128-OD and biotin-N2 is thermodynamically stronger than that between S45-OG and biotin-N1.


    Organizational Affiliation

    Box 351721, Department of Bioengineering, University of Washington, Seattle, WA 98195-1721, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Streptavidin AB127Streptomyces avidiniiMutation(s): 0 
Gene Names: core streptavidin
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download Ideal Coordinates CCD File 
A, B
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNΔH:  89.95999908447266   kJ/mol  BindingDB
BTNΔH:  115.05999755859375   kJ/mol  BindingDB
BTNΔH:  123.01000213623047   kJ/mol  BindingDB
BTNΔH:  66.94000244140625   kJ/mol  BindingDB
BTNΔH:  104.18000030517578   kJ/mol  BindingDB
BTNΔH:  90.37000274658203   kJ/mol  BindingDB
BTNΔH:  117.98999786376953   kJ/mol  BindingDB
BTNKd:  1   nM  BindingDB
BTNΔH:  102.51000213623047   kJ/mol  BindingDB
BTNΔH:  100.41999816894531   kJ/mol  BindingDB
BTNΔH:  107.52999877929688   kJ/mol  BindingDB
BTNΔH:  97.48999786376953   kJ/mol  BindingDB
BTNΔH:  75.30999755859375   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.189 
  • R-Value Observed: 0.128 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.305α = 90
b = 93.414β = 90
c = 103.931γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance