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- PDB-6esd: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -

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Basic information

Entry
Database: PDB / ID: 6esd
TitleCrystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum
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 / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 2017
Title: A semi-synthetic strategy for derivatization of the violacein natural product scaffold
Authors: Lai, H.E. / Chee, S.M. / Morgan, M. / Moore, S. / Polizzi, K. / Freemont, P.
History
DepositionOct 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)94,8626
Polymers93,2202
Non-polymers1,6424
Water88349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SEC-MALS experiment reveals a dimeric assembly of VioA in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-46 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.610, 172.600, 94.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 46609.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: vioA, CV_3274 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.27 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.6→63.78 Å / Num. obs: 38134 / % possible obs: 99 % / Redundancy: 4.55 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04776 / Rrim(I) all: 0.05391 / Net I/σ(I): 24.35
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 4.02 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.34 / Num. unique obs: 3731 / CC1/2: 0.907 / Rrim(I) all: 0.3465 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0V

3x0v


Resolution: 2.6→63.778 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.2588 1958 5.14 %
Rwork0.2088 --
obs0.2113 38070 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→63.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 108 49 6333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096457
X-RAY DIFFRACTIONf_angle_d1.1358783
X-RAY DIFFRACTIONf_dihedral_angle_d13.2723703
X-RAY DIFFRACTIONf_chiral_restr0.055933
X-RAY DIFFRACTIONf_plane_restr0.0061123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66520.39811370.31292542X-RAY DIFFRACTION98
2.6652-2.73720.37141340.29382532X-RAY DIFFRACTION99
2.7372-2.81780.35321320.28572568X-RAY DIFFRACTION99
2.8178-2.90870.36191550.26472533X-RAY DIFFRACTION99
2.9087-3.01270.30511430.26092550X-RAY DIFFRACTION99
3.0127-3.13330.331390.25082507X-RAY DIFFRACTION97
3.1333-3.27590.30681350.23832577X-RAY DIFFRACTION99
3.2759-3.44860.24991300.22552594X-RAY DIFFRACTION99
3.4486-3.66460.28571430.22222586X-RAY DIFFRACTION99
3.6646-3.94760.23221540.19792573X-RAY DIFFRACTION99
3.9476-4.34470.25651430.1682575X-RAY DIFFRACTION98
4.3447-4.97320.1981460.1662622X-RAY DIFFRACTION100
4.9732-6.26490.22561340.19032606X-RAY DIFFRACTION98
6.2649-63.79670.2011330.18422747X-RAY DIFFRACTION98

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