8BY0 | pdb_00008by0

streptavidin mutant S112I K121R with an iridium catalyst for CH activation

• PDB DOI: https://doi.org/10.2210/pdb8BY0/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-11 Released: 2023-12-20 
• Deposition Author(s): Igareta, N.V., Ward, T.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

streptavidin mutant S112I with an iridium catalyst for CH activation

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: 17.53 kDa 
• Atom Count: 1,004 
• Modeled Residue Count: 123 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	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
NOF (Subject of Investigation/LOI)	B [auth A]	tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate C34 H45 Cl Ir N5 O4 S NIFXELQADIYDEE-HVXVAELJSA-L
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.428	α = 90
b = 57.428	β = 90
c = 183.123	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Igareta, N.V., Ward, T.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release