6VD9

Metal-bound C-terminal domain of the CzcD transporter from Cuprividus metallidurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

Currently 6VD9 does not have a validation slider image.


This is version 1.1 of the entry. See complete history


Literature

Structural and functional characterizations of the C-terminal domains of CzcD proteins.

Udagedara, S.R.La Porta, D.M.Spehar, C.Purohit, G.Hein, M.J.A.Fatmous, M.E.Casas Garcia, G.P.Ganio, K.McDevitt, C.A.Maher, M.J.

(2020) J Inorg Biochem 208: 111087-111087

  • DOI: https://doi.org/10.1016/j.jinorgbio.2020.111087
  • Primary Citation of Related Structures:  
    6VD8, 6VD9, 6VDA

  • PubMed Abstract: 

    Zinc is a potent antimicrobial component of the innate immune response at the host-pathogen interface. Bacteria subvert or resist host zinc insults by metal efflux pathways that include cation diffusion facilitator (CDF) proteins. The structural and functional examination of this protein class has been limited, with only the structures of the zinc transporter YiiP proteins from E. coli and Shewanella oneidensis described to date. Here, we determine the metal binding properties, solution quaternary structures and three dimensional architectures of the C-terminal domains of the metal transporter CzcD proteins from Cupriavidus metallidurans, Pseudomonas aeruginosa and Thermotoga maritima. We reveal significant diversity in the metal-binding properties and structures of these proteins and discover a potential novel mechanism for metal-promoted dimerization for the Cupriavidus metallidurans and Pseudomonas aeruginosa proteins.


  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metal cation efflux system protein CzcD
A, B, C, D
75Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: czcDRmet_5979
UniProt
Find proteins for P13512 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore P13512 
Go to UniProtKB:  P13512
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13512
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.76α = 98.78
b = 39.029β = 104.76
c = 63.965γ = 90.09
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report

Currently 6VD9 does not have a validation slider image.



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-06-24 
  • Deposition Author(s): Maher, M.J.

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT180100397

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description