6I86

Crocagin biosynthetic gene J


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster.

Adam, S.Klein, A.Surup, F.Koehnke, J.

(2019) Acta Crystallogr F Struct Biol Commun 75: 205-211

  • DOI: https://doi.org/10.1107/S2053230X19000712
  • Primary Citation of Related Structures:  
    6I86

  • PubMed Abstract: 
  • Natural products often contain interesting new chemical entities that are introduced into the structure of a compound by the enzymatic machinery of the producing organism. The recently described crocagins are novel polycyclic peptides which belong to the class of ribosomally synthesized and post-translationally modified peptide natural products ...

    Natural products often contain interesting new chemical entities that are introduced into the structure of a compound by the enzymatic machinery of the producing organism. The recently described crocagins are novel polycyclic peptides which belong to the class of ribosomally synthesized and post-translationally modified peptide natural products. They have been shown to bind to the conserved prokaryotic carbon-storage regulator A in vitro. In efforts to understand crocagin biosynthesis, the putative biosynthetic genes were expressed and purified. Here, the first crystal structure of a protein from the crocagin-biosynthetic gene cluster, CgnJ, a domain of unknown function protein, is reported. Possible functions of this protein were explored by structural and sequence homology analyses. Even though the sequence homology to proteins in the Protein Data Bank is low, the protein shows significant structural homology to a protein with known function within the competency system of Bacillus subtilis, ComJ, leading to the hypothesis of a similar role of the protein within the producing organism.


    Organizational Affiliation

    Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland, Universität des Saarlandes Gebäude E8.1, 66123 Saarbrücken, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C
156Chondromyces crocatusMutation(s): 0 
Gene Names: CMC5_025600
UniProt
Find proteins for A0A0K1EC30 (Chondromyces crocatus)
Explore A0A0K1EC30 
Go to UniProtKB:  A0A0K1EC30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1EC30
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.56α = 90
b = 132.56β = 90
c = 112.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKO4116_3_1

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references