1JMM | pdb_00001jmm

Crystal structure of the V-region of Streptococcus mutans antigen I/II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.234 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the V-region of Streptococcus mutans Antigen I/II at 2.4 a Resolution Suggests a Sugar Preformed Binding Site

Troffer-Charlier, N.Ogier, J.Moras, D.Cavarelli, J.

(2002) J Mol Biology 318: 179-188

  • DOI: https://doi.org/10.1016/S0022-2836(02)00025-6
  • Primary Citation Related Structures: 
    1JMM

  • PubMed Abstract: 

    Antigens I/II are large multifunctional adhesins from oral viridans streptococci that exert immunomodulatory effects on human cells and play important roles in inflammatory disorders. Among them, Streptococcus mutans plays a major role in the initiation of dental caries. The structure of the V-region (SrV+, residues 464-840) of the antigen I/II of S. mutans has been determined using the multiwavelength anomalous diffraction phasing technique with seleno-methionine-substituted recombinant protein and subsequently refined at 2.4 A resolution. The crystal structure of SrV+ revealed a lectin-like fold that displays a putative preformed carbohydrate-binding site stabilized by a metal ion. Inhibition of this binding site may confer to humans a protection against dental caries and dissemination of the bacteria to extra-oral sites involved in life-threatening inflammatory diseases. This crystal structure constitutes a first step in understanding the structure-function relationship of antigens I/II and may help in delineating new preventive or therapeutic strategies against colonization of the host by oral streptococci.


  • Organizational Affiliation
    • Institut National de la Santé et de la Recherche Médicale U424, Faculté de Chirurgie Dentaire, Université Louis Pasteur, 11 rue Humann, 67085 Strasbourg, France.

Macromolecule Content 

  • Total Structure Weight: 41.64 kDa 
  • Atom Count: 3,171 
  • Modeled Residue Count: 377 
  • Deposited Residue Count: 377 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
protein I/II V-region377Streptococcus mutansMutation(s): 0 
UniProt
Find proteins for P11657 (Streptococcus mutans)
Explore P11657 
Go to UniProtKB:  P11657
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11657
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.234 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.57α = 90
b = 124.57β = 90
c = 147.692γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary