8ZR2 | pdb_00008zr2

Cocrystallization of engineered streptavidin with C9 oligo DNA

• PDB DOI: https://doi.org/10.2210/pdb8ZR2/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-03 Released: 2025-06-04 
• Deposition Author(s): Minamihata, K., Adachi, M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.346 (Depositor), 0.348 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Dual-functional co-crystal of streptavidin and ssDNA: electrostatic assembly with positively charged peptide tags.

Nagatani, A., Minamihata, K., Adachi, M., Wakabayashi, R., Goto, M., Kamiya, N.

(2025) RSC Adv 15: 6817-6822

• PubMed: 40035016 
• DOI: https://doi.org/10.1039/d4ra08326a
• Primary Citation Related Structures: 
  8ZR1, 8ZR2


• PubMed Abstract: 
  

  We have achieved a novel co-crystal in which the dual functions of the protein and single-stranded DNA are maintained by introducing a charged peptide tag at the C-terminus of the protein. The functionalities allowed the co-crystals to be modified with high selectivity. Additionally, we have confirmed that energy transfer occurs between the two molecules modified within the co-crystal. Therefore, this co-crystal has the potential as a novel biomaterial applicable to biosensors.

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Organizational Affiliation: 
• Department of Applied Chemistry, Graduate School of Engineering, Kyushu University 744 Motooka Fukuoka 819-0395 Japan.
Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan.
Department of Quantum Life Science, Graduate School of Science, Chiba University Chiba 263-8522 Japan.
Division of Biotechnology, Center for Future Chemistry, Kyushu University 744 Motooka Fukuoka 819-0395 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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.75 kDa 
• Atom Count: 3,676 
• Modeled Residue Count: 488 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	132	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.346 (Depositor), 0.348 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.937	α = 90
b = 80.986	β = 91.97
c = 77.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Minamihata, K., Adachi, M.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release