6G2P

Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with L-tryptophan

PDB DOI: https://doi.org/10.2210/pdb6G2P/pdb
Entry: 6G2P supersedes: 6ESE

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

Deposited: 2018-03-23 Released: 2018-05-16
Deposition Author(s): Lai, H.E., Morgan, M., Moore, S., Freemont, P.
Funding Organization(s): Imperial College London

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.225
R-Value Work: 0.178
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

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

(2018) bioRxiv

DOI: https://doi.org/10.1101/202523

Macromolecule Content

Total Structure Weight: 95.51 kDa
Atom Count: 6,791
Modelled Residue Count: 826
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent L-tryptophan oxidase VioA	A [auth B], B [auth A]	417	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9S3V1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain G [auth A] MOL2 format, chain C [auth B] MOL2 format, chain G [auth A] mmCIF format, chain C [auth B] mmCIF format, chain G [auth A]	C [auth B], G [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth B] Focus chain G [auth A] Interactions & Density Focus chain C [auth B] Focus chain G [auth A]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain H [auth A] MOL2 format, chain D [auth B] MOL2 format, chain H [auth A] mmCIF format, chain D [auth B] mmCIF format, chain H [auth A]	D [auth B], H [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain D [auth B] Focus chain H [auth A] Interactions & Density Focus chain D [auth B] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain I [auth A] MOL2 format, chain E [auth B] MOL2 format, chain I [auth A] mmCIF format, chain E [auth B] mmCIF format, chain I [auth A]	E [auth B], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain J [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth A] mmCIF format, chain F [auth B] mmCIF format, chain J [auth A]	F [auth B], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain J [auth A] Interactions & Density Focus chain F [auth B] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.225
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.092	α = 90
b = 175.338	β = 90
c = 94.436	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

This entry supersedes: 6ESE

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

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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Help and Resources

6G2P

Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with L-tryptophan

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)