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- PDB-7z99: Crystal structure of F191M variant of Variovorax paradoxus indole... -

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Basic information

Entry
Database: PDB / ID: 7z99
TitleCrystal structure of F191M variant of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with methyl phenyl sulfoxide
ComponentsPutative dehydrogenase/oxygenase subunit (Flavoprotein)
KeywordsOXIDOREDUCTASE / FAD-dependent monooxygenase / styrene monooxygenase / StyA1 / IMO
Function / homologyStyrene monooxygenase StyA, putative substrate binding domain / Styrene monooxygenase A putative substrate binding domain / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / [(S)-methylsulfinyl]benzene / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsKratky, J. / Weisse, R. / Strater, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations.
Authors: Kratky, J. / Eggerichs, D. / Heine, T. / Hofmann, S. / Sowa, P. / Weisse, R.H. / Tischler, D. / Strater, N.
History
DepositionMar 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3754
Polymers47,3091
Non-polymers1,0663
Water4,864270
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7498
Polymers94,6172
Non-polymers2,1326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5560 Å2
ΔGint-23 kcal/mol
Surface area29730 Å2
Unit cell
Length a, b, c (Å)93.468, 93.468, 110.316
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative dehydrogenase/oxygenase subunit (Flavoprotein)


Mass: 47308.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus EPS (bacteria) / Strain: EPS / Gene: Varpa_4903 / Production host: Escherichia coli (E. coli) / References: UniProt: E6V140
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-IH0 / [(S)-methylsulfinyl]benzene / (S)-methyl phenylsulfoxide


Mass: 140.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8OS
Details: The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be ...Details: The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be modeled each in the three low-energy rotamers of the -S(=O)CH3 group into the electron density with comparable fit.
Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsThe crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl ...The crystals were incubated with a racemic mixture of methyl phenyl sulfoxide. only (s)-methyl phenyl sulfoxide is modelled in this coordinate file. Both configurations, (r) and (s), can be modeled each in the three low-energy rotamers of the -S(=O)CH3 group into the electron density with comparable fit.

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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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Na-acetate pH 5, 1400 mM Na-malonate, 1 mM DTT, 3 mM FAD, 1 mM racemic methyl phenyl sulfoxide, cryo: 15 % (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 2.101424 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.101424 Å / Relative weight: 1
ReflectionResolution: 1.92→46.73 Å / Num. obs: 38322 / % possible obs: 88.9 % / Redundancy: 16.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Rrim(I) all: 0.081 / Net I/σ(I): 23.4 / Num. measured all: 645788 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.963.61.00921205870.4870.5291.1531.121.1
9-46.7315.20.04673774840.9990.0110.04754.799.5

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7z4x

7z4x


Resolution: 1.92→45.58 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 1936 5.06 %
Rwork0.1588 36343 -
obs0.1605 38279 89.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.73 Å2 / Biso mean: 36.3183 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 1.92→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 101 270 3509
Biso mean--37.15 36.56 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.970.3684200.307167869823
1.97-2.020.2564710.23191509158052
2.02-2.080.25631130.21232220233377
2.08-2.150.25631160.18532815293197
2.15-2.230.19731360.181329123048100
2.23-2.320.22611280.167828973025100
2.32-2.420.20911360.17962882301899
2.42-2.550.20971850.166328693054100
2.55-2.710.2061480.17528983046100
2.71-2.920.21431950.17228513046100
2.92-3.210.23321650.17952903306899
3.21-3.680.1761800.143428933073100
3.68-4.630.1671670.125229613128100
4.63-45.580.15251760.1483055323199

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