Crystal structure of shwanavidin (F43A) - biotin complex

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1074/jbc.M112.357186
  • Primary Citation of Related Structures:  
    3SZH, 3SZI, 3SZJ, 3T2W, 3T2X

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Avidin/streptavidin122Shewanella denitrificans OS217Mutation(s): 1 
Gene Names: Sden_0912
Find proteins for Q12QS6 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Explore Q12QS6 
Go to UniProtKB:  Q12QS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12QS6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BTN

Download Ideal Coordinates CCD File 
B [auth A]BIOTIN
C10 H16 N2 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN Binding MOAD:  3T2W Kd: 64 (nM) from 1 assay(s)
PDBBind:  3T2W Kd: 35 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.212α = 90
b = 63.212β = 90
c = 65.83γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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