3DE9

Crystal Structure of a Trimeric Cytochrome cb562 Assembly Induced by Nickel Coordination

• PDB DOI: https://doi.org/10.2210/pdb3DE9/pdb

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


• Deposited: 2008-06-08 Released: 2009-04-21 
• Deposition Author(s): Salgado, E.N., Lewis, R.A., Rheingold, A.L., Tezcan, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.278 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 

Literature

Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination.

Salgado, E.N., Lewis, R.A., Mossin, S., Rheingold, A.L., Tezcan, F.A.

(2009) Inorg Chem 48: 2726-2728

• PubMed: 19267481 
• DOI: https://doi.org/10.1021/ic9001237
• Primary Citation of Related Structures:  
  3DE8, 3DE9


• PubMed Abstract: 
  

  We describe the metal-dependent self-assembly of symmetrical protein homooligomers from protein building blocks that feature appropriately engineered metal-chelating motifs on their surfaces. Crystallographic studies indicate that the same four-helix-bundle protein construct, MBPC-1, can self-assemble into C(2) and C(3) symmetrical assemblies dictated by Cu(II) and Ni(II) coordination, respectively. The symmetry inherent in metal coordination can thus be directly applied to biological self-assembly.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 12.52 kDa 
• Atom Count: 920 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	106	Escherichia coli	Mutation(s): 5  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NI	B [auth A], C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.278 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.042	α = 90
b = 51.042	β = 90
c = 121.971	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
APEX	data collection
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Salgado, E.N., Lewis, R.A., Rheingold, A.L., Tezcan, F.A.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection