6LNG

Rapid crystallization of streptavidin using charged peptides

• PDB DOI: https://doi.org/10.2210/pdb6LNG/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-30 Released: 2020-03-18 
• Deposition Author(s): Minamihata, K., Tsukamoto, K., Adachi, M., Shimizu, R., Mishina, M., Kuroki, R., Nagamune, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Genetically fused charged peptides induce rapid crystallization of proteins.

Minamihata, K., Tsukamoto, K., Adachi, M., Shimizu, R., Mishina, M., Kuroki, R., Nagamune, T.

(2020) Chem Commun (Camb) 56: 3891-3894

• PubMed: 32134050 
• DOI: https://doi.org/10.1039/c9cc09529b
• Primary Citation of Related Structures:  
  6LNG


• PubMed Abstract: 
  

  We utilized electrostatic interaction to induce rapid crystallization of streptavidin. Simply mixing streptavidins possessing either a positively or negatively charged peptide at their C-terminus generated diffraction-quality crystals in a few hours. We modified the streptavidin crystals with fluorescent molecules using biotin, demonstrating the concept of protein crystals as functional biomaterials.

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Organizational Affiliation: 

Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan. [e-mail].

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: 79.04 kDa 
• Atom Count: 6,178 
• Modelled Residue Count: 732 
• Deposited Residue Count: 750 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D, E, F	125	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.2929992676	α = 90
b = 80.8290023804	β = 99.8460006714
c = 132.647994995	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Minamihata, K., Tsukamoto, K., Adachi, M., Shimizu, R., Mishina, M., Kuroki, R., Nagamune, T.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description