3HNJ

Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Metal templated design of protein interfaces.

Salgado, E.N.Ambroggio, X.I.Brodin, J.D.Lewis, R.A.Kuhlman, B.Tezcan, F.A.

(2010) Proc.Natl.Acad.Sci.USA 107: 1827-1832

  • DOI: 10.1073/pnas.0906852107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and ...

    Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event. Using a folded monomeric protein, cytochrome cb(562), as a building block we show that its non-self-associating surface can be made self-associating through a minimal number of mutations that enable Zn coordination. The protein interfaces in the resulting Zn-directed, D(2)-symmetrical tetramer are subsequently redesigned, yielding unique protein architectures that self-assemble in the presence or absence of metals. Aside from its evolutionary implications, MeTIR provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562
A, B, C, D
106Escherichia coliMutation(s): 17 
Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.448α = 90.00
b = 65.316β = 104.70
c = 70.773γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance