6FW8 | pdb_00006fw8

Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 5-Methyl-L-Tryptophan

PDB DOI: https://doi.org/10.2210/pdb6FW8/pdb

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

Deposited: 2018-03-05 Released: 2019-02-13
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: 2.40 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A GenoChemetic strategy for derivatization of the violacein natural product scaffold

Lai, H.E., Obled, A.M.C., Chee, S.M., Morgan, R.M., Sharma, S.V., Moore, S.J., Polizzi, K.M., Goss, R.J.M., Freemont, P.S.

(2019) bioRxiv

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

Macromolecule Content

Total Structure Weight: 95.42 kDa
Atom Count: 6,707
Modelled Residue Count: 834
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 LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain C [auth B] MOL2 format, chain F [auth A] MOL2 format, chain C [auth B] mmCIF format, chain F [auth A] mmCIF format, chain C [auth B]	C [auth B], F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
D0Q Query on D0Q Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain G [auth A] MOL2 format, chain D [auth B] MOL2 format, chain G [auth A] mmCIF format, chain D [auth B] mmCIF format, chain G [auth A]	D [auth B], G [auth A]	5-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ HUNCSWANZMJLPM-JTQLQIEISA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Interactions & Density Focus chain D [auth B] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth B] mmCIF format, chain H [auth A]	E [auth B], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain H [auth A] Interactions & Density Focus chain E [auth B] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.13	α = 90
b = 174.088	β = 90
c = 93.922	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: 2019-02-13

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2019-02-13
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-01-17
Changes: Refinement description

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Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 5-Methyl-L-Tryptophan

A GenoChemetic strategy for derivatization of the violacein natural product scaffold

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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