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- PDB-6fw8: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -

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Basic information

Entry
Database: PDB / ID: 6fw8
TitleCrystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 5-Methyl-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
5-methyl-L-tryptophan / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)95,4188
Polymers93,3622
Non-polymers2,0566
Water1,74797
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SEC-MALS revealed VioA exists as homodimer in buffer solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-43 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.130, 174.088, 93.922
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: 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-D0Q / 5-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O2
#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.: 97 / 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: 3.31 Å3/Da / Density % sol: 62.82 %
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: 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: 2.4→58.875 Å / Num. obs: 48699 / % possible obs: 98 % / Redundancy: 6.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1053 / Rrim(I) all: 0.1147 / Net I/σ(I): 9.44
Reflection shellResolution: 2.4→2.449 Å / Redundancy: 6 % / Num. unique obs: 4768 / % possible all: 100

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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: 6ESD

6esd


Resolution: 2.4→58.875 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 2327 4.87 %
Rwork0.1882 --
obs0.1909 47819 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→58.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 140 97 6627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086820
X-RAY DIFFRACTIONf_angle_d1.0239276
X-RAY DIFFRACTIONf_dihedral_angle_d15.3833992
X-RAY DIFFRACTIONf_chiral_restr0.053971
X-RAY DIFFRACTIONf_plane_restr0.0061187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3998-2.44880.42811230.3612481X-RAY DIFFRACTION93
2.4488-2.5020.42111450.32412567X-RAY DIFFRACTION96
2.502-2.56020.35171250.30012621X-RAY DIFFRACTION96
2.5602-2.62430.34071210.27962579X-RAY DIFFRACTION96
2.6243-2.69520.361360.26352621X-RAY DIFFRACTION97
2.6952-2.77450.33081600.26582590X-RAY DIFFRACTION98
2.7745-2.86410.34251290.24022687X-RAY DIFFRACTION98
2.8641-2.96640.2871370.22862664X-RAY DIFFRACTION98
2.9664-3.08520.30081400.21252663X-RAY DIFFRACTION99
3.0852-3.22560.28831310.20572712X-RAY DIFFRACTION99
3.2256-3.39560.2611400.19222698X-RAY DIFFRACTION100
3.3956-3.60840.24541530.19592719X-RAY DIFFRACTION100
3.6084-3.88690.25751490.17042710X-RAY DIFFRACTION100
3.8869-4.2780.18331400.14622731X-RAY DIFFRACTION100
4.278-4.89670.17411330.14012751X-RAY DIFFRACTION100
4.8967-6.16830.21281500.1672779X-RAY DIFFRACTION100
6.1683-58.89320.21141150.1692919X-RAY DIFFRACTION99

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