3X00 | pdb_00003x00

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

• PDB DOI: https://doi.org/10.2210/pdb3X00/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-09 Released: 2015-01-21 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.188 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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 79: 640-642

• PubMed: 25560769 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

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 (software)

Macromolecule Content

• Total Structure Weight: 62.79 kDa 
• Atom Count: 4,405 
• Modelled Residue Count: 496 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	147	Streptomyces avidinii	Mutation(s): 9
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
ZOF	E [auth A], F [auth B], H [auth C], I [auth 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
EDN	G [auth B], J [auth D]	ETHANE-1,2-DIAMINE C2 H8 N2 PIICEJLVQHRZGT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZOF	BindingDB:  3X00	Kd: 154 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.188 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.354	α = 90
b = 77.377	β = 90
c = 174.122	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description