6WZ1

Mn-bound structure of an engineered protein trimer, TriCyt3

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

  • Deposited: 2020-05-13 Released: 2020-09-16 
  • Deposition Author(s): Tezcan, F.A., Kakkis, A.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites.

Kakkis, A.Gagnon, D.Esselborn, J.Britt, R.D.Tezcan, F.A.

(2020) Angew Chem Int Ed Engl 59: 21940-21944

  • DOI: https://doi.org/10.1002/anie.202009226
  • Primary Citation of Related Structures:  
    6WYU, 6WZ0, 6WZ1, 6WZ2, 6WZ3, 6WZ7, 6WZA, 6WZC, 6X7E, 6X8X

  • PubMed Abstract: 

    To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb 562 ) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb 562 surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1) 3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2) 3 and (TriCyt3) 3 with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562
A, B, C
106Escherichia coliMutation(s): 16 
Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
M [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
L [auth B],
O [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
N [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.759α = 90
b = 77.392β = 110.7
c = 47.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE1607145
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM112584-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description