Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.53 kDa 
• Atom Count: 3800 
• Modelled Residue Count: 478 
• Deposited Residue Count: 508 
• Unique protein chains: 1

1KFF

An engineered streptavidin with improved affinity for the strep-tag II peptide: apo-SAM1

• PDB DOI: 10.2210/pdb1KFF/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-20 Released: 2002-04-03 
• Deposition Author(s): Korndoerfer, I.P., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.229 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site.

Korndorfer, I.P., Skerra, A.

(2002) Protein Sci 11: 883-893

• PubMed: 11910031 
• DOI: 10.1110/ps.4150102
• Primary Citation of Related Structures:  
  1KFF, 1KL3, 1KL4, 1KL5


• PubMed Abstract: 
  

The Strep-tag II is a nine-amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants '1' and '2,' which had been engineered for 10-fold higher affinity towards the Strep-tag II. Both streptavidin mutants carry mutations at positions 44, 45, and 47, that is, in a flexible loop region close to the binding site. The crystal structures of the two apo-proteins and their complexes with the Strep-tag II peptide were refined at resolutions below 2 A. Both in the presence and absence of the peptide, the lid-like loop next to the ligand pocket--comprising residues 45 through 52--adopts an 'open' conformation in all four subunits within the asymmetric unit. The same loop was previously described to be disordered in the wild-type apo-streptavidin and to close over the pocket upon complexation of the natural ligand biotin. Our findings suggest that stabilization of the 'open' loop conformation in the absence of a ligand abolishes the need for conformational rearrangement prior to the docking of the voluminous peptide. Because no direct contacts between the flexible part of the loop and the peptide ligand were detected, it seems likely that the higher affinity of the two streptavidin mutants for the Strep-tag II is caused by a predominantly entropic mechanism.

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Organizational Affiliation: 

Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
streptavidin	A, B, C, D	127	Streptomyces avidinii	Mutation(s): 3
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.229 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.419	α = 90
b = 86.916	β = 98.9
c = 47.196	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-20 
• Released Date: 2002-04-03 
Deposition Author(s): Korndoerfer, I.P., Skerra, A.

Revision History  

• Version 1.0: 2002-04-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references