8FX6 | pdb_00008fx6

Non-ribosomal PCP-C didomain (amide stabilised leucine) acceptor bound state

• PDB DOI: https://doi.org/10.2210/pdb8FX6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-24 Released: 2023-06-21 
• Deposition Author(s): Ho, Y.T.C., Cryle, M.J.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis.

Ho, Y.T.C., Kaczmarski, J.A., Tailhades, J., Izore, T., Steer, D.L., Schittenhelm, R.B., Tosin, M., Jackson, C.J., Cryle, M.J.

(2023) Chem Commun (Camb) 59: 8234-8237

• PubMed: 37310188 
• DOI: https://doi.org/10.1039/d3cc01578e
• Primary Citation Related Structures: 
  8FX6, 8FX7


• PubMed Abstract: 
  

  Nonribosomal peptide synthetases produce many important peptide natural products and are centred around carrier proteins (CPs) that deliver intermediates to various catalytic domains. We show that the replacement of CP substrate thioesters by stabilised ester analogues leads to active condensation domain complexes, whereas amide stabilisation generates non-functional complexes.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. [e-mail].
EMBL Australia, Monash University, Clayton, VIC 3800, Australia.
ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia.
Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australia.
Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia.
Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC 3800, Australia.
Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 114.49 kDa 
• Atom Count: 8,199 
• Modeled Residue Count: 1,027 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCP-C didomain	A, B	520	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_1867
UniProt
Find proteins for Q47NR9 (Thermobifida fusca (strain YX)) Explore Q47NR9  Go to UniProtKB:  Q47NR9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YCK (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]-L-leucinamide C17 H35 N4 O8 P OHVFVHYHCFDMRA-JSGCOSHPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.719	α = 90
b = 105.084	β = 90
c = 108.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Ho, Y.T.C., Cryle, M.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP190101272
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1140619

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2023-07-05
  Changes: Database references
• Version 1.2: 2023-07-12
  Changes: Data collection, Database references
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-11-13
  Changes: Structure summary