4BG2

X-ray Crystal Structure of PatF from Prochloron didemni

• PDB DOI: https://doi.org/10.2210/pdb4BG2/pdb

• Classification: TRANSFERASE
• Organism(s): Prochloron didemni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-22 Released: 2013-04-03 
• Deposition Author(s): Bent, A.F., Koehnke, J., Houssen, W.E., Smith, M.C.M., Jaspars, M., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.221 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structure of Patf from Prochloron Didemni.

Bent, A.F., Koehnke, J., Houssen, W.E., Smith, M.C.M., Jaspars, M., Naismith, J.H.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 618

• PubMed: 23722837 
• DOI: https://doi.org/10.1107/S1744309113012931
• Primary Citation of Related Structures:  
  4BG2


• PubMed Abstract: 
  

  Patellamides are macrocyclic peptides with potent biological effects and are a subset of the cyanobactins. Cyanobactins are natural products that are produced by a series of enzymatic transformations and a common modification is the addition of a prenyl group. Puzzlingly, the pathway for patellamides in Prochloron didemni contains a gene, patF, with homology to prenylases, but patellamides are not themselves prenylated. The structure of the protein PatF was cloned, expressed, purified and determined. Prenylase activity could not be demonstrated for the protein, and examination of the structure revealed changes in side-chain identity at the active site. It is suggested that these changes have inactivated the protein. Attempts to mutate these residues led to unfolded protein.

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Organizational Affiliation: 

Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.38 kDa 
• Atom Count: 4,951 
• Modelled Residue Count: 595 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PATF	A, B	321	Prochloron didemni	Mutation(s): 0
UniProt
Find proteins for Q52QJ2 (Prochloron didemni) Explore Q52QJ2  Go to UniProtKB:  Q52QJ2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.221 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.08	α = 90
b = 135.8	β = 118.54
c = 48.738	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Bent, A.F., Koehnke, J., Houssen, W.E., Smith, M.C.M., Jaspars, M., Naismith, J.H.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2013-11-06
  Changes: Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary