4BE6

V. cholera biofilm scaffolding protein RbmA

• PDB DOI: https://doi.org/10.2210/pdb4BE6/pdb

• Classification: CELL ADHESION
• Organism(s): Vibrio cholerae MJ-1236
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-06 Released: 2013-12-18 
• Deposition Author(s): Maestre-Reyna, M., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Starting Model: experimental

Literature

Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae.

Maestre-Reyna, M., Wu, W.-J., Wang, A.H.-J.

(2013) PLoS One 8: 82458

• PubMed: 24340031 
• DOI: https://doi.org/10.1371/journal.pone.0082458
• Primary Citation of Related Structures:  
  4BE5, 4BE6, 4BEI


• PubMed Abstract: 
  

  V. cholerae can form sessile biofilms associated with abiotic surfaces, cyanobacteria, zoo-plankton, mollusks, or crustaceans. Along with the vibrio polysaccharide, secreted proteins of the rbm gene cluster are key to the biofilm ultrastructure. Here we provide a thorough structural characterization of RbmA, a protein involved in mediating cell-cell and cell-biofilm contacts. We correlate our structural findings with initial ligand specificity screening results, NMR protein-ligand interaction analysis, and complement our results with a full biocomputational study.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 57.75 kDa 
• Atom Count: 4,130 
• Modelled Residue Count: 459 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RBMA	A, B	262	Vibrio cholerae MJ-1236	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	C [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.162 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.22	α = 90
b = 118.22	β = 90
c = 104.984	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Maestre-Reyna, M., Wang, A.H.-J.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2014-01-08
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description