6ESD

Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb6ESD/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-20 Released: 2017-12-06 
• Deposition Author(s): Lai, H.E., Morgan, M., Moore, S., Freemont, P.
• Funding Organization(s): Imperial College London

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

A semi-synthetic strategy for derivatization of the violacein natural product scaffold

Lai, H.E., Chee, S.M., Morgan, M., Moore, S., Polizzi, K., Freemont, P.

(2017) bioRxiv 

• DOI: https://doi.org/10.1101/202523

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 94.86 kDa 
• Atom Count: 6,333 
• Modelled Residue Count: 827 
• Deposited Residue Count: 832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent L-tryptophan oxidase VioA	A [auth B], B [auth A]	416	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: vioA, CV_3274 EC: 1.4.3.23
UniProt
Find proteins for Q9S3V1 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q9S3V1  Go to UniProtKB:  Q9S3V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth B], E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL	D [auth B], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.61	α = 90
b = 172.6	β = 90
c = 94.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Lai, H.E., Morgan, M., Moore, S., Freemont, P.

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Funding Organization	Location	Grant Number
Imperial College London	United Kingdom	President's PhD Scholarship

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description