4PQ1 | pdb_00004pq1

Crystal structure and functional implications of a DsbF homologue from Corynebacterium diphtheriae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Structure of a DsbF homologue from Corynebacterium diphtheriae.

Um, S.H., Kim, J.S., Lee, K., Ha, N.C.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1167-1172

  • DOI: https://doi.org/10.1107/S2053230X14016355
  • Primary Citation Related Structures: 
    4PQ1

  • PubMed Abstract: 

    Disulfide-bond formation, mediated by the Dsb family of proteins, is important in the correct folding of secreted or extracellular proteins in bacteria. In Gram-negative bacteria, disulfide bonds are introduced into the folding proteins in the periplasm by DsbA. DsbE from Escherichia coli has been implicated in the reduction of disulfide bonds in the maturation of cytochrome c. The Gram-positive bacterium Mycobacterium tuberculosis encodes DsbE and its homologue DsbF, the structures of which have been determined. However, the two mycobacterial proteins are able to oxidatively fold a protein in vitro, unlike DsbE from E. coli. In this study, the crystal structure of a DsbE or DsbF homologue protein from Corynebacterium diphtheriae has been determined, which revealed a thioredoxin-like domain with a typical CXXC active site. Structural comparison with M. tuberculosis DsbF would help in understanding the function of the C. diphtheriae protein.

    • Organizational Affiliation: 
    • Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 34.61 kDa 
  • Atom Count: 2,606 
  • Modeled Residue Count: 315 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative electron transport related protein
A, B
158Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP0411
UniProt
Find proteins for Q6NJJ0 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NJJ0 
Go to UniProtKB:  Q6NJJ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NJJ0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.103α = 90
b = 36.162β = 67.89
c = 62.522γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-01-01
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary