oligopeptide-binding protein OppA

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile

Yoon, H.J.Kim, H.J.Mikami, B.Yu, Y.G.Lee, H.H.

(2016) Extremophiles 20: 723-731

  • DOI: https://doi.org/10.1007/s00792-016-0861-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Oligopeptide-binding proteins (Opps) are part of the ATP-binding cassette system, playing a crucial role in nutrient uptake and sensing the external environment in bacteria, including hyperthermophiles. Opps serve as a binding platform for diverse peptides; however, how these peptides are recognized by Opps is still largely unknown and few crystal structures of Opps from hyperthermophiles have been determined. To facilitate such an understanding, the crystal structure of a putative Opp, OppA from Thermotoga maritima (TmOppA), was solved at 2.6-Å resolution in the open conformation. TmOppA is composed of three domains. The N-terminal domain consists of twelve strands, nine helices, and four 310 helices, and the C-terminal domain consists of five strands, ten helices, and one 310 helix. These two domains are connected by the linker domain, which consists of two strands, three helices, and three 310 helices. Based on structural comparisons of TmOppA with other OppAs and binding studies, we suggest that TmOppA might be a periplasmic Opp. The most distinct feature of TmOppA is the insertion of two helices, which are lacking in other OppAs. A cavity volume between the N-terminal and C-terminal domains is suggested to be responsible for binding peptides of various lengths.

  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative633Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_0056
Find proteins for Q9WXR2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXR2 
Go to UniProtKB:  Q9WXR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WXR2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.494α = 90
b = 190.494β = 90
c = 133.269γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references