5WBB | pdb_00005wbb

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - S112A

• PDB DOI: https://doi.org/10.2210/pdb5WBB/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-28 Released: 2017-11-22 
• Deposition Author(s): Mann, S.I., Heinisch, T., Ward, T.R., Borovik, A.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins.

Mann, S.I., Heinisch, T., Ward, T.R., Borovik, A.S.

(2017) J Am Chem Soc 139: 17289-17292

• PubMed: 29117678 
• DOI: https://doi.org/10.1021/jacs.7b10452
• Primary Citation Related Structures: 
  5WBA, 5WBB, 5WBD, 6ANX


• PubMed Abstract: 
  

  Copper-hydroperoxido species (Cu ^II -OOH) have been proposed to be key intermediates in biological and synthetic oxidations. Using biotin-streptavidin (Sav) technology, artificial copper proteins have been developed to stabilize a Cu ^II -OOH complex in solution and in crystallo. Stability is achieved because the Sav host provides a local environment around the Cu-OOH that includes a network of hydrogen bonds to the hydroperoxido ligand. Systematic deletions of individual hydrogen bonds to the Cu-OOH complex were accomplished using different Sav variants and demonstrated that stability is achieved with a single hydrogen bond to the proximal O-atom of the hydroperoxido ligand: changing this interaction to only include the distal O-atom produced a reactive variant that oxidized an external substrate.

---

Organizational Affiliation: 
• Department of Chemistry, University of California , 1102 Natural Science II, Irvine, California 92697, United States.
Department of Chemistry, University of Basel , P.O. Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.37 kDa 
• Atom Count: 1,128 
• Modeled Residue Count: 125 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	159	Streptomyces avidinii	Mutation(s): 1
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SQ1	B [auth A]	[N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide]copper C26 H36 Cu N6 O2 S SAHQKCHSOKYSAG-LTWAPREQSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.64	α = 90
b = 57.64	β = 90
c = 183.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Mann, S.I., Heinisch, T., Ward, T.R., Borovik, A.S.

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description