1R9U

Refined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 24 
  • Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Biosynthetic Uniform 13C,15N-Labelling of Zervamicin Iib. Complete 13C and 15N NMR Assignment.

Ovchinnikova, T.V., Shenkarev, Z.O., Yakimenko, Z.A., Svishcheva, N.V., Tagaev, A.A., Skladnev, D.A., Arseniev, A.S.

(2003) J Pept Sci 9: 817-826

  • DOI: https://doi.org/10.1002/psc.499
  • Primary Citation of Related Structures:  
    1R9U

  • PubMed Abstract: 

    Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.

    • Organizational Affiliation: 

    Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. ovch@ibch.ru


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ZERVAMICIN IIB17Emericellopsis salmosynnemataMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
HYP
Query on HYP
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
PHL
Query on PHL
A
L-PEPTIDE LINKINGC9 H13 N OPHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChains NameType/Class2D Diagram3D Interactions
PRD_000159
Query on PRD_000159
A
Zervamicin IIBPeptaibol / Antibiotic
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 24 
  • Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2018-10-10
    Changes: Data collection, Database references, Experimental preparation, Other, Structure summary