1STP | pdb_00001stp

STRUCTURAL ORIGINS OF HIGH-AFFINITY BIOTIN BINDING TO STREPTAVIDIN

• PDB DOI: https://doi.org/10.2210/pdb1STP/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Mutation(s): No 


• Deposited: 1992-03-12 Released: 1992-10-15 
• Deposition Author(s): Weber, P.C., Salemme, F.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Structural origins of high-affinity biotin binding to streptavidin.

Weber, P.C., Ohlendorf, D.H., Wendoloski, J.J., Salemme, F.R.

(1989) Science 243: 85-88

• PubMed: 2911722 
• DOI: https://doi.org/10.1126/science.2911722
• Primary Citation of Related Structures:  
  1STP


• PubMed Abstract: 
  

  The high affinity of the noncovalent interaction between biotin and streptavidin forms the basis for many diagnostic assays that require the formation of an irreversible and specific linkage between biological macromolecules. Comparison of the refined crystal structures of apo and a streptavidin:biotin complex shows that the high affinity results from several factors. These factors include the formation of multiple hydrogen bonds and van der Waals interactions between biotin and the protein, together with the ordering of surface polypeptide loops that bury the biotin in the protein interior. Structural alterations at the biotin binding site produce quaternary changes in the streptavidin tetramer. These changes apparently propagate through cooperative deformations in the twisted beta sheets that link tetramer subunits.

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Organizational Affiliation: 

Central Research & Development Department, E. I. du Pont de Neumours and Company, Inc., Wilmington, DE 19880-0228.

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: 16.75 kDa 
• Atom Count: 1,001 
• Modeled Residue Count: 121 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STREPTAVIDIN COMPLEX WITH BIOTIN	A	159	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	B [auth A]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	BindingDB:  1STP	Kd: 0 (nM) from 1 assay(s)
		ΔH: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.4	α = 90
b = 99.4	β = 90
c = 125.8	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-10-15 
Deposition Author(s): Weber, P.C., Salemme, F.R.

Revision History  

• Version 1.0: 1992-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other