3FOP

A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Hexagonal Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly.

Radford, R.J.Tezcan, F.A.

(2009) J Am Chem Soc 131: 9136-9137

  • DOI: 10.1021/ja9000695
  • Primary Citation of Related Structures:  
    3FOO, 3FOP

  • PubMed Abstract: 
  • We previously devised a strategy (metal-directed protein self-assembly, MDPSA) that utilizes the simultaneous stability, lability, and directionality of metal-ligand bonds to drive protein-protein interactions. Here we show that both the structural a ...

    We previously devised a strategy (metal-directed protein self-assembly, MDPSA) that utilizes the simultaneous stability, lability, and directionality of metal-ligand bonds to drive protein-protein interactions. Here we show that both the structural and functional scopes of MDPSA can be broadened by incorporation of non-natural metal-chelating ligands onto protein surfaces. A cytochrome cb(562) variant, MBP-Phen1, which features a covalently attached phenanthroline (Phen) group on its surface, self-assembles into an unusual triangular architecture (Ni(3):MBP-Phen1(3)) upon binding Ni as a result of specific Phen-protein interactions. The crystal structure of Ni(3):MBP-Phen1(3) reveals that the Phen group is buried in a small pocket on the protein surface, which results in an unsaturated Ni coordination environment.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0356, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562AB106Escherichia coliMutation(s): 7 
Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PXX
Query on PXX

Download CCD File 
A, B
N-1,10-phenanthrolin-5-ylacetamide
C14 H11 N3 O
AAJXINSCZMZERD-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.897α = 90
b = 104.897β = 90
c = 107.925γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance