Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.33 kDa 
• Atom Count: 1076 
• Modelled Residue Count: 125 
• Deposited Residue Count: 153 
• Unique protein chains: 1

3RE5

Crystal structure of R4-6 streptavidin

• PDB DOI: 10.2210/pdb3RE5/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-02 Released: 2011-07-06 
• Deposition Author(s): Malashkevich, V.N., Magalhaes, M., Czecster, C.M., Guan, R., Levy, M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.

Magalhaes, M.L., Czekster, C.M., Guan, R., Malashkevich, V.N., Almo, S.C., Levy, M.

(2011) Protein Sci 20: 1145-1154

• PubMed: 21520321 
• DOI: 10.1002/pro.642
• Primary Citation of Related Structures:  
  3RDM, 3RDO, 3RDQ, 3RDS, 3RDU, 3RDX, 3RE5, 3RE6


• PubMed Abstract: 
  

We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a ∼10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	153	Streptomyces avidinii	Mutation(s): 5
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.471	α = 90
b = 57.471	β = 90
c = 173.612	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-02 
• Released Date: 2011-07-06 
Deposition Author(s): Malashkevich, V.N., Magalhaes, M., Czecster, C.M., Guan, R., Levy, M., Almo, S.C.

Revision History  

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary