3DE9

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


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 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562A106Escherichia coliMutation(s): 5 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
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 = 51.042α = 90
b = 51.042β = 90
c = 121.971γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
APEXdata collection
SAINTdata reduction
SADABSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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