6EOW | pdb_00006eow

Structure of Raspberry Ketone Synthase with Hydroxybenzalacetone

• PDB DOI: https://doi.org/10.2210/pdb6EOW/pdb

• Classification: TRANSFERASE
• Organism(s): Rubus idaeus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-10 Released: 2018-10-24 
• Deposition Author(s): Tosi, T., Moore, S.J., Freemont, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

A cell-free synthetic biochemistry platform for raspberry ketone production

Moore, S.J., Tosi, T., Hleba, Y.B., Bell, D., Polizzi, K.M., Freemont, P.S.

(2018) bioRxiv 

• DOI: https://doi.org/10.1101/202341

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 166.28 kDa 
• Atom Count: 11,256 
• Modeled Residue Count: 1,329 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketone/zingerone synthase 1	A, B, C, D	368	Rubus idaeus	Mutation(s): 0  Gene Names: ZS1 EC: 1.3.1.74
UniProt
Find proteins for G1FCG0 (Rubus idaeus) Explore G1FCG0  Go to UniProtKB:  G1FCG0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
BKZ	F [auth B], H [auth C], J [auth D]	4-(4-hydroxyphenyl)butan-2-one C10 H12 O2 NJGBTKGETPDVIK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.038	α = 77.68
b = 81.733	β = 85.13
c = 93.046	γ = 72.7

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Tosi, T., Moore, S.J., Freemont, P.S.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description