6UBL

Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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This is version 1.1 of the entry. See complete history


Literature

The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina.

Kosgei, A.J.Miller, M.D.Bhardwaj, M.Xu, W.Thorson, J.S.Van Lanen, S.G.Phillips Jr., G.N.

(2022) Acta Crystallogr F Struct Biol Commun 78: 1-7

  • DOI: https://doi.org/10.1107/S2053230X21012322
  • Primary Citation of Related Structures:  
    6UBL, 7ML6, 7MSY

  • PubMed Abstract: 

    Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded β-barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is central to the synthesis of the ten-membered ring of the enediyne core.


  • Organizational Affiliation

    Department of Biosciences, Rice University, Houston, TX 77251, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DynF
A, B
211Micromonospora chersinaMutation(s): 0 
Gene Names: GA0070603_4197
UniProt
Find proteins for B2BM43 (Micromonospora chersina)
Explore B2BM43 
Go to UniProtKB:  B2BM43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2BM43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.83α = 90
b = 116.126β = 90
c = 129.877γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA217255
National Science Foundation (NSF, United States)United StatesSTC-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references