Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.65 kDa 
• Atom Count: 850 
• Residue Count: 91 
• Unique protein chains: 1

4U9E

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3

• DOI: 10.2210/pdb4U9E/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-08-06 Released: 2015-01-21 
• Deposition Author(s): Tezcan, F.A., Song, W.J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Literature

A designed supramolecular protein assembly with in vivo enzymatic activity

Song, W.J., Tezcan, A.F.

(2014) Science 346: 1525

• PubMed: 25525249 
• DOI: 10.1126/science.1259680
• Primary Citation of Related Structures:  
  4U9D, 4U9E


• PubMed Abstract: 
  

The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-β-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-β-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(k(cat)/K(m))/k(uncat)] for ampicillin hydrolysis of 2.3 × 10(6) and features the emergence of a highly mobile loop near the active site, a key component of natural β-lactamases to enable substrate interactions.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	106	Escherichia coli	Mutation(s): 16  Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.313	α = 90
b = 92.213	β = 90
c = 98.599	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-08-06 
• Released Date: 2015-01-21 
Deposition Author(s): Tezcan, F.A., Song, W.J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE1306646

Revision History 

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence