Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.13 kDa 
• Atom Count: 1739 
• Residue Count: 207 
• Unique protein chains: 1

1OTM

Calcium-binding mutant of the internalin B LRR domain

• DOI: 10.2210/pdb1OTM/pdb

• Classification: CELL ADHESION
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-03-21 Released: 2004-03-30 
• Deposition Author(s): Marino, M., Copp, J., Dramsi, S., Chapman, T., van der Geer, P., Cossart, P., Ghosh, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.206 

Literature

Characterization of the calcium-binding sites of Listeria monocytogenes InlB

Marino, M., Banerjee, M., Copp, J., Dramsi, S., Chapman, T., Van Der Geer, P., Cossart, P., Ghosh, P.

(2004) Biochem Biophys Res Commun 316: 379-386

• PubMed: 15020228 
• DOI: 10.1016/j.bbrc.2004.02.064
• Primary Citation of Related Structures:  
  1OTM, 1OTO, 1OTN


• PubMed Abstract: 
  

The Listeria monocytogenes protein InlB promotes invasion of mammalian cells through activation of the receptor tyrosine kinase Met. The InlB N-cap, a approximately 40 residue part of the domain that binds Met, was previously observed to bind two calcium ions in a novel and unusually exposed manner. Because subsequent work raised questions about the existence of these calcium-binding sites, we assayed calcium binding in solution to the InlB N-cap. We show that calcium ions are bound with dissociation constants in the low micromolar range at the two identified sites, and that the sites interact with one another. We demonstrate that the calcium ions are not required for structure, and also find that they have no appreciable effect on Met activation or intracellular invasion. Therefore, our results indicate that the sites are fortuitous in InlB, but also suggest that the simple architecture of the sites may be adaptable for protein engineering purposes.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
internalin B	A	236	Listeria monocytogenes	Mutation(s): 6
Find proteins for P0DQD2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P0DQD2  Go to UniProtKB:  P0DQD2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.296	α = 90
b = 57.215	β = 90
c = 84.84	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-21 
• Released Date: 2004-03-30 
Deposition Author(s): Marino, M., Copp, J., Dramsi, S., Chapman, T., van der Geer, P., Cossart, P., Ghosh, P.

Revision History 

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description