8Y28 | pdb_00008y28

X-ray crystal structure of ALiS5-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method

• PDB DOI: https://doi.org/10.2210/pdb8Y28/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Streptomyces avidinii
• Mutation(s): No 


• Deposited: 2024-01-25 Released: 2025-01-29 
• Deposition Author(s): Higashiura, A., Yamamoto, A., Sugiyama, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Binding competition between substrates and cryoprotectants in protein crystals directly observed by a hybrid method of in-gel crystallization and high-pressure cryo-cooling in X-ray crystallography

Higashiura, A., Sugiyama, S.

To be published.

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: 51.58 kDa 
• Atom Count: 4,269 
• Modeled Residue Count: 476 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	121	Streptomyces avidinii	Mutation(s): 0
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
GOL	E [auth A], G [auth B], H [auth C], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A], I [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.666	α = 90
b = 85.553	β = 98.87
c = 58.343	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Higashiura, A., Yamamoto, A., Sugiyama, S.

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Funding Organization	Location	Grant Number
Other private	Japan	--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release