[English] 日本語
Yorodumi
- PDB-6fw9: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fw9
TitleCrystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 6-Fluoro-L-Tryptophan
ComponentsFlavin-dependent L-tryptophan oxidase VioA
KeywordsBIOSYNTHETIC PROTEIN / Violacein biosynthesis / L-tryptophan oxidase
Function / homology
Function and homology information


7-chloro-L-tryptophan oxidase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 6-FLUORO-L-TRYPTOPHAN / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.739 Å
AuthorsLai, H.E. / Morgan, M. / Moore, S. / Freemont, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
CitationJournal: Biorxiv / Year: 2019
Title: A GenoChemetic strategy for derivatization of the violacein natural product scaffold
Authors: 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.
History
DepositionMar 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Advisory / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Flavin-dependent L-tryptophan oxidase VioA
A: Flavin-dependent L-tryptophan oxidase VioA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4268
Polymers93,3622
Non-polymers2,0646
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS shows that VioA exists as homodimer in buffer solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-43 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.478, 174.322, 93.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Flavin-dependent L-tryptophan oxidase VioA


Mass: 46680.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Gene: vioA, CV_3274 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FT6 / 6-FLUORO-L-TRYPTOPHAN / (S)-2-AMINO-3-(6-FLUORO-1H-INDOL-3-YL)PROPANOIC ACID


Type: L-peptide linking / Mass: 222.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11FN2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 9% PEG 8000 and 9% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.739→63.86 Å / Num. obs: 33026 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.1456 / Rrim(I) all: 0.1587 / Net I/σ(I): 8.05
Reflection shellResolution: 2.739→2.828 Å / Redundancy: 6.3 % / Num. unique obs: 3237 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESE

6ese
PDB Unreleased entry


Resolution: 2.739→63.857 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 1595 4.89 %
Rwork0.197 --
obs0.2 32621 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.739→63.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 140 118 6598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096766
X-RAY DIFFRACTIONf_angle_d1.1029219
X-RAY DIFFRACTIONf_dihedral_angle_d14.6673930
X-RAY DIFFRACTIONf_chiral_restr0.058970
X-RAY DIFFRACTIONf_plane_restr0.0061179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7391-2.82750.41191380.34232679X-RAY DIFFRACTION95
2.8275-2.92860.38751490.33912725X-RAY DIFFRACTION97
2.9286-3.04590.40281420.30992776X-RAY DIFFRACTION98
3.0459-3.18450.33211270.25812789X-RAY DIFFRACTION99
3.1845-3.35240.32091430.23412822X-RAY DIFFRACTION99
3.3524-3.56240.29961380.21492824X-RAY DIFFRACTION99
3.5624-3.83740.29231620.19042810X-RAY DIFFRACTION99
3.8374-4.22350.18211600.14912838X-RAY DIFFRACTION100
4.2235-4.83450.22851490.14262862X-RAY DIFFRACTION100
4.8345-6.09020.22371360.16782902X-RAY DIFFRACTION100
6.0902-63.87440.21521510.18242999X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more