3V10

Crystal structure of the collagen binding domain of Erysipelothrix rhusiopathiae surface protein RspB

• PDB DOI: https://doi.org/10.2210/pdb3V10/pdb

• Classification: CELL ADHESION
• Organism(s): Erysipelothrix rhusiopathiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-09 Released: 2012-10-24 
• Deposition Author(s): Ponnuraj, K., Swarmistha devi, A., Ogawa, Y., Shimoji, Y., Subramainan, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.225 

Literature

Collagen adhesin-nanoparticle interaction impairs adhesin's ligand binding mechanism

Devi, A.S., Ogawa, Y., Shimoji, Y., Balakumar, S., Ponnuraj, K.

(2012) Biochim Biophys Acta 1820: 819-828

• PubMed: 22538248 
• DOI: https://doi.org/10.1016/j.bbagen.2012.04.006
• Primary Citation of Related Structures:  
  3V10


• PubMed Abstract: 
  

  Pathogenic bacteria specifically recognize extracellular matrix (ECM) molecules of the host (e.g. collagen, fibrinogen and fibronectin) through their surface proteins known as MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules) and initiate colonization. On implantation, biomaterials easily get coated with these ECM molecules and the MSCRAMMs mediate bacterial adherence to biomaterials. With the rapid rise in antibiotic resistance, designing alternative strategies to reduce/eliminate bacterial colonization is absolutely essential.

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Organizational Affiliation: 

Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai-600 025, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.4 kDa 
• Atom Count: 5,230 
• Modelled Residue Count: 619 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhusiopathiae surface protein B	A, B	321	Erysipelothrix rhusiopathiae	Mutation(s): 0  Gene Names: rspB
UniProt
Find proteins for Q83VG5 (Erysipelothrix rhusiopathiae) Explore Q83VG5  Go to UniProtKB:  Q83VG5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.17	α = 90
b = 67.39	β = 92.82
c = 102.41	γ = 90

Software Package:

Software Name	Purpose
Auto-Rickshaw	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Ponnuraj, K., Swarmistha devi, A., Ogawa, Y., Shimoji, Y., Subramainan, B.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references