1O84 | pdb_00001o84

Crystal Structure of Bacteriocin AS-48. N-decyl-beta-D-maltoside Bound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.256 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1O84

This is version 2.1 of the entry. See complete history

Literature

Structure of Bacteriocin as-48: From Soluble State to Membrane Bound State

Sanchez-Barrena, M.J.Martinez-Ripoll, M.Galvez, A.Valdivia, E.Maqueda, M.Cruz, V.Albert, A.

(2003) J Mol Biology 334: 541

  • DOI: https://doi.org/10.1016/j.jmb.2003.09.060
  • Primary Citation Related Structures: 
    1O82, 1O83, 1O84

  • PubMed Abstract: 

    The bacteriocin AS-48 is a membrane-interacting peptide, which displays a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. The NMR structure of AS-48 at pH 3 has been solved. The analysis of this structure suggests that the mechanism of AS-48 anti-bacterial activity involves the accumulation of positively charged molecules at the membrane surface leading to a disruption of the membrane potential. Here, we report the high-resolution crystal structure of AS-48 and sedimentation equilibrium experiments showing that this bacteriocin is able to adopt different oligomeric structures according to the physicochemical environment. The analysis of these structures suggests a mechanism for molecular function of AS-48 involving a transition from a water-soluble form to a membrane-bound state upon membrane binding.


  • Organizational Affiliation
    • Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006, Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 15.41 kDa 
  • Atom Count: 1,097 
  • Modeled Residue Count: 140 
  • Deposited Residue Count: 140 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PEPTIDE ANTIBIOTIC AS-48
A, B
70Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for Q47765 (Enterococcus faecalis)
Explore Q47765 
Go to UniProtKB:  Q47765
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47765
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D10

Query on D10



Download:Ideal Coordinates CCD File
F [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.256 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.488α = 90
b = 76.488β = 90
c = 51.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-10-16
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Structure summary