5D9E | pdb_00005d9e

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 (Depositor), 0.110 (DCC) 
  • R-Value Work: 
    0.098 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 
    0.099 (Depositor) 

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 (Depositor), 0.110 (DCC) 
  • R-Value Work:  0.098 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 0.099 (Depositor) 
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

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View more in-depth experimental data
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