9AVK

Structure of long Rib domain from Limosilactobacillus reuteri


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the long Rib domain of the LPXTG-anchored surface protein from Limosilactobacillus reuteri.

Xue, Y.Wu, Z.Kang, X.

(2024) Acta Crystallogr F Struct Biol Commun 80: 92-97

  • DOI: https://doi.org/10.1107/S2053230X24003868
  • Primary Citation of Related Structures:  
    9AVK

  • PubMed Abstract: 

    The Rib domain, which is often found as tandem-repeat structural modules in surface proteins of Gram-positive bacteria, plays important roles in mediating interactions of bacteria with their environments and hosts. A comprehensive structural analysis of various Rib domains is essential to fully understand their impact on the structure and functionality of these bacterial adhesins. To date, structural information has been limited for this expansive group of domains. In this study, the high-resolution crystal structure of the second member of the long Rib domain, a unique subclass within the Rib-domain family, derived from Limosilactobacillus reuteri is presented. The data not only demonstrate a highly conserved structure within the long Rib domain, but also highlight an evolutionary convergence in structural architecture with other modular domains found in cell-adhesion molecules.


  • Organizational Affiliation

    Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YSIRK signal domain/LPXTG anchor domain surface protein104Limosilactobacillus reuteriMutation(s): 0 
Gene Names: DB325_02015
UniProt
Find proteins for A0A2T5Q5G6 (Limosilactobacillus reuteri)
Explore A0A2T5Q5G6 
Go to UniProtKB:  A0A2T5Q5G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T5Q5G6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.161α = 90
b = 36.161β = 90
c = 126.332γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SADABSdata scaling
SAINTdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22074070

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Database references