6AUE | pdb_00006aue

Artificial Metalloproteins Containing a Co4O4 Active Site - 2xm-S112Y-b

• PDB DOI: https://doi.org/10.2210/pdb6AUE/pdb

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


• Deposited: 2017-08-31 Released: 2018-02-28 
• Deposition Author(s): Olshansky, L., Vallapurakal, J., Huerta-Lavorie, R., Nguyen, A.I., Tilley, T.D., Borovik, A.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Artificial Metalloproteins Containing Co

Olshansky, L., Huerta-Lavorie, R., Nguyen, A.I., Vallapurackal, J., Furst, A., Tilley, T.D., Borovik, A.S.

(2018) J Am Chem Soc 140: 2739-2742

• PubMed: 29401385 
• DOI: https://doi.org/10.1021/jacs.7b13052
• Primary Citation Related Structures: 
  6AUC, 6AUE, 6AUH, 6AUL, 6AUO


• PubMed Abstract: 
  

  Artificial metalloproteins (ArMs) containing Co ₄ O ₄ cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co ^III -OH ₂ moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e ^- /1H ⁺ chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co ₄ O ₄ active site provided a single H-bond to one of a set of cofacial Co ^III -OH ₂ groups. With this variant, multi-e ^- /multi-H ⁺ chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. With structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co ₄ O ₄ core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e ^- /multi-H ⁺ reactivity.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States.
Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States.
Chemical Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.

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: 17.63 kDa 
• Atom Count: 1,050 
• Modeled Residue Count: 121 
• 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): 3
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
OL3	B [auth A]	N-biotin-C-Co4(mu3-O)4(OAc)(Py)4(H2O)3-beta-alanine C35 H45 Co4 N7 O13 S JXTIQCHHLFQVFH-VNIQYHKJSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.945	α = 90
b = 57.945	β = 90
c = 184.565	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Olshansky, L., Vallapurakal, J., Huerta-Lavorie, R., Nguyen, A.I., Tilley, T.D., Borovik, A.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM120349

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references
• Version 1.2: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description