7EK9 | pdb_00007ek9

Crystal structure of apo streptavidin at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb7EK9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Streptomyces avidinii
• Mutation(s): No 


• Deposited: 2021-04-04 Released: 2021-09-29 
• Deposition Author(s): DeMirci, H., Ayan, E., Destan, E., Ertem, F.B.
• Funding Organization(s): National Science Foundation (NSF, United States), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.187 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of apo streptavidin at cryogenic temperature

DeMirci, H.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 52.4 kDa 
• Atom Count: 4,462 
• Modeled Residue Count: 482 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	123	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
MPD (Subject of Investigation/LOI)	H [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD (Subject of Investigation/LOI)	E [auth A], F [auth C], G [auth D]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.187 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.373	α = 90
b = 85.946	β = 98.73
c = 58.188	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): DeMirci, H., Ayan, E., Destan, E., Ertem, F.B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-1231306
Other government	Turkey	118C270

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection