2BC3 | pdb_00002bc3

T7-tagged full-length streptavidin

• PDB DOI: https://doi.org/10.2210/pdb2BC3/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-18 Released: 2005-10-25 
• Deposition Author(s): Stenkamp, R.E., Le Trong, I., Ward, T.R., Humbert, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.243 (Depositor) 
• R-Value Work: 
  0.175 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Analysis of a Full-length Streptavidin with Its C-terminal Polypeptide Bound in the Biotin Binding Site.

Le Trong, I., Humbert, N., Ward, T.R., Stenkamp, R.E.

(2006) J Mol Biology 356: 738-745

• PubMed: 16384581 
• DOI: https://doi.org/10.1016/j.jmb.2005.11.086
• Primary Citation Related Structures: 
  2BC3


• PubMed Abstract: 
  

  The structure of a full-length streptavidin has been determined at 1.7 A resolution and shows that the 20 residue extension at the C terminus forms a well-ordered polypeptide loop on the surface of the tetramer. Residues 150-153 of the extension are bound to the ligand-binding site, possibly competing with exogenous ligands. The binding mode of these residues is compared with that of biotin and peptidic ligands. The observed structure helps to rationalize the observations that full-length mature streptavidin binds biotinylated macromolecules with reduced affinity.

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Organizational Affiliation: 
• Departments of Biological Structure and Biochemistry and the Biomolecular Structure Center, University of Washington, Box 357420, Seattle, WA 98195-7420, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.42 kDa 
• Atom Count: 2,434 
• Modeled Residue Count: 286 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	159	Streptomyces avidinii	Mutation(s): 0
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
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.243 (Depositor) 
• R-Value Work:  0.175 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.704	α = 90
b = 82.391	β = 103.48
c = 46.71	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Stenkamp, R.E., Le Trong, I., Ward, T.R., Humbert, N.

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Data collection, Refinement description