7ZXZ | pdb_00007zxz

dithiol-ligand bound to streptavidin

• PDB DOI: https://doi.org/10.2210/pdb7ZXZ/pdb

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


• Deposited: 2022-05-23 Released: 2022-06-15 
• Deposition Author(s): Igareta, N.V., Ward, T.R.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

dithiol-ligand bound to streptavidin

Igareta, N.V., Ward, T.R.

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 33.85 kDa 
• Atom Count: 2,124 
• Modeled Residue Count: 247 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	158	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
K9R (Subject of Investigation/LOI)	D [auth A], E [auth B]	5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[(1~{R},3~{S})-3-[3,5-bis(sulfanylmethyl)phenyl]-2,4-bis(oxidanylidene)cyclopentyl]pentanamide C23 H29 N3 O4 S3 UYYZXEJGUBQKBA-JSCGBJRHSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.324	α = 90
b = 80.79	β = 104.317
c = 46.657	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Igareta, N.V., Ward, T.R.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description