2VSQ

Structure of surfactin A synthetase C (SrfA-C), a nonribosomal peptide synthetase termination module

• PDB DOI: https://doi.org/10.2210/pdb2VSQ/pdb

• Classification: LIGASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-04-29 Released: 2008-07-08 
• Deposition Author(s): Tanovic, A., Samel, S.A., Essen, L.-O., Marahiel, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Starting Models: experimental

Literature

Crystal structure of the termination module of a nonribosomal peptide synthetase.

Tanovic, A., Samel, S.A., Essen, L.O., Marahiel, M.A.

(2008) Science 321: 659-663

• PubMed: 18583577 
• DOI: https://doi.org/10.1126/science.1159850
• Primary Citation of Related Structures:  
  2VSQ


• PubMed Abstract: 
  

  Nonribosomal peptide synthetases (NRPSs) are modular multidomain enzymes that act as an assembly line to catalyze the biosynthesis of complex natural products. The crystal structure of the 144-kilodalton Bacillus subtilis termination module SrfA-C was solved at 2.6 angstrom resolution. The adenylation and condensation domains of SrfA-C associate closely to form a catalytic platform, with their active sites on the same side of the platform. The peptidyl carrier protein domain is flexibly tethered to this platform and thus can move with its substrate-loaded 4'-phosphopantetheine arm between the active site of the adenylation domain and the donor side of the condensation domain. The SrfA-C crystal structure has implications for the rational redesign of NRPSs as a means of producing novel bioactive peptides.

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Organizational Affiliation: 

Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D35032 Marburg, Germany.

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: 147.67 kDa 
• Atom Count: 10,109 
• Modelled Residue Count: 1,273 
• Deposited Residue Count: 1,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SURFACTIN SYNTHETASE SUBUNIT 3	A	1,304	Bacillus subtilis	Mutation(s): 1
UniProt
Find proteins for Q08787 (Bacillus subtilis (strain 168)) Explore Q08787  Go to UniProtKB:  Q08787

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEU	B [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.106	α = 90
b = 106.562	β = 97.35
c = 92.401	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Tanovic, A., Samel, S.A., Essen, L.-O., Marahiel, M.A.

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2019-01-30
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description