5D9E | pdb_00005d9e

Crystal Structure of the Proline-rich Lasso Peptide Caulosegnin II

• PDB DOI: https://doi.org/10.2210/pdb5D9E/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Caulobacter segnis ATCC 21756
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-18 Released: 2016-02-17 
• Deposition Author(s): Fage, C.D., Hegemann, J.D., Harms, K., Marahiel, M.A.
• Funding Organization(s): German Research Foundation, LOEWE-Zentrum fuer Synthetische Mikrobiologie

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free: 
  0.107 (Depositor), 0.105 (DCC) 
• R-Value Work: 
  0.098 (Depositor), 0.099 (DCC) 
• R-Value Observed: 
  0.099 (Depositor) 

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

• PubMed: 26863937 
• DOI: https://doi.org/10.1039/c6mb00081a
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry/Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 2.05 kDa 
• Atom Count: 176 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caulosegnin II	A	19	Caulobacter segnis ATCC 21756	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
SME	A	MET	Oxidation	C5 H11 N O3 S

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.86 Å
• R-Value Free:  0.107 (Depositor), 0.105 (DCC) 
• R-Value Work:  0.098 (Depositor), 0.099 (DCC) 
• R-Value Observed: 0.099 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 15.71	α = 90
b = 19.312	β = 90
c = 39.674	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Fage, C.D., Hegemann, J.D., Harms, K., Marahiel, M.A.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--
LOEWE-Zentrum fuer Synthetische Mikrobiologie	Germany	--

Revision History  

• 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
• Version 1.4: 2025-04-09
  Changes: Data collection, Database references, Structure summary