3X00

Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (Bis-IMNtail) at 1.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report



Literature

Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant

Kawato, T.Mizohata, E.Shimizu, Y.Meshizuka, T.Yamamoto, T.Takasu, N.Matsuoka, M.Matsumura, H.Kodama, T.Kanai, M.Doi, H.Inoue, T.Sugiyama, A.

(2015) Biosci Biotechnol Biochem 

  • DOI: 10.1080/09168451.2014.991692
  • Primary Citation of Related Structures:  
    3X00

  • PubMed Abstract: 
  • The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for n ...

    The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.


    Organizational Affiliation

    a Division of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita , Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
StreptavidinABCD147Streptomyces avidiniiMutation(s): 9 
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZOF
Query on ZOF

Download CCD File 
A, B, C, D
6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid
C16 H28 N4 O3 S
IAJKFHSLWUNBII-HUBLWGQQSA-N
 Ligand Interaction
EDN
Query on EDN

Download CCD File 
B, D
ETHANE-1,2-DIAMINE
C2 H8 N2
PIICEJLVQHRZGT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZOFKd:  154   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.354α = 90
b = 77.377β = 90
c = 174.122γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release