3T2W

Crystal structure of shwanavidin (F43A) - biotin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment.

Meir, A.Bayer, E.A.Livnah, O.

(2012) J.Biol.Chem. 287: 17951-17962

  • DOI: 10.1074/jbc.M112.357186
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive di ...

    Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive disulfide bridge were shown to account for the high affinity toward biotin. Phe-43 emulates the function and position of the critical intermonomeric Trp that characterizes the tetrameric avidins but is lacking in shwanavidin. The 18 copies of the apo-monomer revealed distinctive snapshots of L3,4 and Phe-43, providing rare insight into loop flexibility, binding site accessibility, and psychrophilic adaptation. Nevertheless, as in all avidins, shwanavidin also displays high thermostability properties. The unique features of shwanavidin may provide a platform for the design of a long sought after monovalent form of avidin, which would be ideal for novel types of biotechnological application.


    Organizational Affiliation

    Department of Biological Chemistry, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Avidin/streptavidin
A
122Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)Mutation(s): 1 
Find proteins for Q12QS6 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Go to UniProtKB:  Q12QS6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download SDF File 
Download CCD File 
A
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd: 1450 nM BINDINGMOAD
BTNKd: 35 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.212α = 90.00
b = 63.212β = 90.00
c = 65.830γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-23 
  • Released Date: 2012-04-11 
  • Deposition Author(s): Livnah, O., Meir, A.

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Database references
  • Version 1.2: 2012-06-13
    Type: Database references
  • Version 1.3: 2016-10-12
    Type: Advisory