4BEI

V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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This is version 1.3 of the entry. See complete history. 


Literature

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

Maestre-Reyna, M., Wu, W., Wang, A.H.

(2013) PLoS One 8: 82458

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RBMA
A, B, C, D, E
A, B, C, D, E, F, G, H
262Vibrio cholerae MJ-1236Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O4B
Query on O4B
Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
L [auth C]
M [auth D]
O [auth E]
I [auth A],
K [auth B],
L [auth C],
M [auth D],
O [auth E],
Q [auth F],
S [auth G],
T [auth H]
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
C12 H24 O6
XEZNGIUYQVAUSS-UHFFFAOYSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
J [auth A],
N [auth D],
P [auth E],
R [auth F]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.885α = 90
b = 136.885β = 90
c = 116.312γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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