5MKC | pdb_00005mkc

Crystal structure of the RrgA Jo.In complex

• PDB DOI: https://doi.org/10.2210/pdb5MKC/pdb

• Classification: CELL ADHESION
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-03 Released: 2017-03-15 
• Deposition Author(s): Bonnet, J., Cartannaz, J., Tourcier, G., Contreras-Martel, C., Kleman, J.P., Fenel, D., Schoehn, G., Morlot, C., Vernet, T., Di Guilmi, A.M.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.243 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin.

Bonnet, J., Cartannaz, J., Tourcier, G., Contreras-Martel, C., Kleman, J.P., Morlot, C., Vernet, T., Di Guilmi, A.M.

(2017) Sci Rep 7: 43564-43564

• PubMed: 28252635 
• DOI: https://doi.org/10.1038/srep43564
• Primary Citation Related Structures: 
  5MKC


• PubMed Abstract: 
  

  Unusual intramolecular cross-links present in adhesins from Gram-positive bacteria have been used to develop a generic process amenable to biotechnology applications. Based on the crystal structure of RrgA, the Streptococcus pneumoniae pilus adhesin, we provide evidence that two engineered protein fragments retain their ability to associate covalently with high specificity, in vivo and in vitro, once isolated from the parent protein. We determined the optimal conditions for the assembly of the complex and we solved its crystal structure at 2 Å. Furthermore, we demonstrate biotechnological applications related to antibody production, nanoassembly and cell-surface labeling based on this process we named Bio Molecular Welding.

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Organizational Affiliation: 
• Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 158.58 kDa 
• Atom Count: 10,949 
• Modeled Residue Count: 1,240 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell wall surface anchor family protein (Jo),Cell wall surface anchor family protein (In)	A, B, C, D, E, F	232	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ERS409372_01591, ERS515225_01161, ERS020491_02171
UniProt
Find proteins for A0A0H2UNT6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UNT6  Go to UniProtKB:  A0A0H2UNT6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F], X [auth F], Y [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	J [auth A], S [auth D], Z [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	AA [auth F], O [auth C], V [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.243 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.541	α = 90
b = 134.571	β = 90
c = 144.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Bonnet, J., Cartannaz, J., Tourcier, G., Contreras-Martel, C., Kleman, J.P., Fenel, D., Schoehn, G., Morlot, C., Vernet, T., Di Guilmi, A.M.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-11-BSV8-005-01
French National Research Agency	France	ANR-12-BSV3-0003-01

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2018-11-21
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-06-05
  Changes: Advisory, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Structure summary