2QIF

Crystal structure of a metallochaperone with a tetranuclear Cu(I) cluster

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.175 
  • R-Value Observed: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A tetranuclear Cu(I) cluster in the metallochaperone protein CopZ.

Hearnshaw, S., West, C., Singleton, C., Zhou, L., Kihlken, M.A., Strange, R.W., Le Brun, N.E., Hemmings, A.M.

(2009) Biochemistry 48: 9324-9326

  • DOI: 10.1021/bi9011995
  • Primary Citation of Related Structures:  
    2QIF

  • PubMed Abstract: 

    • Copper trafficking proteins and copper-sensitive regulators are often found to be able to bind multiple Cu(I) ions in the form of Cu(I) clusters. We have determined the high-resolution X-ray crystal structure of an Atx1-like copper chaperone protein ...

    Copper trafficking proteins and copper-sensitive regulators are often found to be able to bind multiple Cu(I) ions in the form of Cu(I) clusters. We have determined the high-resolution X-ray crystal structure of an Atx1-like copper chaperone protein from Bacillus subtilis containing a novel tetranuclear Cu(I) cluster. The identities and oxidation states of the cluster ions were established unambiguously by refinement of X-ray energy-dependent anomalous scattering factors. The [Cu(4)(S-Cys)(4)(N-His)(2)] cluster geometry provides new structural insights into not only the binding of multiple cuprous ions by metallochaperones but also protein-associated tetranuclear Cu(I) clusters, including those found in eukaryotic copper-responsive transcription factors.

    Related Citations: 
    • Copper-mediated dimerization of CopZ, a predicted copper chaperone from Bacillus subtilis
      Kihlken, M.A., Leech, A.P., Le Brun, N.E.
      (2002) Biochem J 368: 729
    Organizational Affiliation: 

    Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper chaperone copZA, B69N/AMutation(s): 0 
Gene Names: copZ, yvgY
Find proteins for O32221 (Bacillus subtilis (strain 168))
Explore O32221 
Go to UniProtKB:  O32221
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CU1
Query on CU1
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A, B
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.175 
  • R-Value Observed: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.44α = 90
b = 74.692β = 101.55
c = 41.212γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SHELXphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description