5MAS

Peptaibol Bergofungin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution.

Gessmann, R.Axford, D.Bruckner, H.Berg, A.Petratos, K.

(2017) Acta Crystallogr F Struct Biol Commun 73: 95-100

  • DOI: 10.1107/S2053230X17001236

  • PubMed Abstract: 
  • Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This i ...

    Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 310-helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.


    Organizational Affiliation

    IMBB/FORTH, 70013 Heraklion, Crete, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bergofungin A
A
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
AIB
Query on AIB
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
DIV
Query on DIV
A
D-PEPTIDE LINKINGC5 H11 N O2

--

PHL
Query on PHL
A
L-PEPTIDE LINKINGC9 H13 N OPHE
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.131 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.275α = 90.00
b = 8.932β = 119.72
c = 24.604γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SHELXSphasing
XDSdata reduction
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references