7EFD | pdb_00007efd

1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40 e/A^2 total dose)

• PDB DOI: https://doi.org/10.2210/pdb7EFD/pdb
• EM Map EMD-31084: EMDB EMDataResource

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


• Deposited: 2021-03-21 Released: 2021-04-28 
• Deposition Author(s): Hiraizumi, M., Yamashita, K., Nishizawa, T., Kotecha, A., Nureki, O.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40e/A^2 total dose)

Hiraizumi, M.

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 (software)

Macromolecule Content 

• Total Structure Weight: 19.09 kDa 
• Atom Count: 1,001 
• Modeled Residue Count: 120 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	183	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
BTN	B [auth A]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	BindingDB:  7EFD	Kd: 0 (nM) from 1 assay(s)
		ΔG: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	REFMAC	5.8.0272

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Hiraizumi, M., Yamashita, K., Nishizawa, T., Kotecha, A., Nureki, O.

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Refinement description