5MAS

Peptaibol Bergofungin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.131 
  • R-Value Observed: 0.103 

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
  • Primary Citation of Related Structures:  
    5MAS

  • 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 is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin 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 3 10 -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 LengthOrganismDetailsImage
Bergofungin AA16Emericellopsis donezkiiMutation(s): 0 
UniProt
Find proteins for A0A1U7Q1Y9 (Emericellopsis donezkii)
Explore A0A1U7Q1Y9 
Go to UniProtKB:  A0A1U7Q1Y9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
AL-PEPTIDE LINKINGC4 H9 N O2ALA
HYP
Query on HYP
AL-PEPTIDE LINKINGC5 H9 N O3PRO
PHL
Query on PHL
AL-PEPTIDE LINKINGC9 H13 N OPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.84 Å
  • R-Value Free: 0.131 
  • R-Value Observed: 0.103 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.275α = 90
b = 8.932β = 119.72
c = 24.604γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
XDSdata reduction
SHELXSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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