Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.61 kDa 
• Atom Count: 1075 
• Modelled Residue Count: 113 
• Deposited Residue Count: 123 
• Unique protein chains: 1

3OON

The structure of an outer membrance protein from Borrelia burgdorferi B31

• PDB DOI: 10.2210/pdb3OON/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Borreliella burgdorferi B31
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-31 Released: 2010-09-22 
• Deposition Author(s): Fan, Y., Bigelow, L., Feldman, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi.

Tan, K., Deatherage Kaiser, B.L., Wu, R., Cuff, M., Fan, Y., Bigelow, L., Jedrzejczak, R.P., Adkins, J.N., Cort, J.R., Babnigg, G., Joachimiak, A.

(2017) Protein Sci 26: 1738-1748

• PubMed: 28580643 
• DOI: 10.1002/pro.3209
• Primary Citation of Related Structures:  
  3OON, 4RHA, 5VES


• PubMed Abstract: 
  

Salmonella enterica serovar Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel transmembrane domain and a C-terminal domain (OmpA ^CTD ). The OmpA ^CTD and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM. Here we present the first crystal structures of the OmpA ^CTD from two pathogens: S. typhimurium (STOmpA ^CTD ) in open and closed forms and causative agent of Lyme Disease Borrelia burgdorferi (BbOmpA ^CTD ), in closed form. In the open form of STOmpA ^CTD , an aspartate residue from a long β2-α3 loop points into the binding pocket, suggesting that an anion group such as a carboxylate group from PG is favored at the binding site. In the closed form of STOmpA ^CTD and in the structure of BbOmpA ^CTD , a sulfate group from the crystallization buffer is tightly bound at the binding site. The differences between the closed and open forms of STOmpA ^CTD , suggest a large conformational change that includes an extension of α3 helix by ordering a part of β2-α3 loop. We propose that the sulfate anion observed in these structures mimics the carboxylate group of PG when bound to STOmpA ^CTD suggesting PG-anchoring mechanism. In addition, the binding of PG or a ligand mimic may enhance dimerization of STOmpA ^CTD , or possibly that of full length STOmpA.

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Organizational Affiliation: 

Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein (Tpn50)	A	123	Borreliella burgdorferi B31	Mutation(s): 0  Gene Names: BB_0167
UniProt
Find proteins for O51189 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O51189  Go to UniProtKB:  O51189

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.089	α = 90
b = 74.784	β = 90
c = 66.76	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-31 
• Released Date: 2010-09-22 
Deposition Author(s): Fan, Y., Bigelow, L., Feldman, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-04-08
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2019-12-04
  Changes: Database references, Derived calculations