5D9E

Crystal Structure of the Proline-rich Lasso Peptide Caulosegnin II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.107 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II.

Hegemann, J.D.Fage, C.D.Zhu, S.Harms, K.Di Leva, F.S.Novellino, E.Marinelli, L.Marahiel, M.A.

(2016) Mol Biosyst 12: 1106-1109

  • DOI: https://doi.org/10.1039/c6mb00081a
  • Primary Citation of Related Structures:  
    5D9E

  • PubMed Abstract: 

    Lasso peptides are fascinating natural products with a unique structural fold that can exhibit tremendous thermal stability. Here, we investigate factors responsible for the thermal stability of caulosegnin II. By employing X-ray crystallography, mutational analysis and molecular dynamics simulations, the ring residue proline 8 was proven to be crucial for thermal stability.


  • Organizational Affiliation

    Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany. marahiel@staff.uni-marburg.de.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caulosegnin II19Caulobacter segnis ATCC 21756Mutation(s): 0 
Gene Names: Cseg_2567
UniProt
Find proteins for D5VKJ8 (Caulobacter segnis (strain ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059))
Explore D5VKJ8 
Go to UniProtKB:  D5VKJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5VKJ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SME
Query on SME
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.107 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 15.71α = 90
b = 19.312β = 90
c = 39.674γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--
LOEWE-Zentrum fuer Synthetische MikrobiologieGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2016-03-30
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations