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- PDB-7zca: Crystal structure of the F191M/F201A variant of Variovorax parado... -

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Basic information

Entry
Database: PDB / ID: 7zca
TitleCrystal structure of the F191M/F201A variant of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with benzyl 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 / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / phenylsulfinylmethylbenzene / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 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 26, 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)48,5105
Polymers47,2321
Non-polymers1,2774
Water5,963331
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)97,01910
Polymers94,4652
Non-polymers2,5548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5970 Å2
ΔGint-25 kcal/mol
Surface area29710 Å2
Unit cell
Length a, b, c (Å)93.589, 93.589, 111.152
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: 47232.496 Da / Num. of mol.: 1 / Mutation: F191M, F201A
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-IKF / phenylsulfinylmethylbenzene


Mass: 216.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.66 %
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 6-bromoindole, 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: 14.1 / Wavelength: 1.79687 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.79687 Å / Relative weight: 1
ReflectionResolution: 1.68→46.79 Å / Num. obs: 58636 / % possible obs: 90.3 % / Redundancy: 15.1 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Net I/σ(I): 27.6 / Num. measured all: 884857 / Scaling rejects: 4
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
1.68-1.712.51.67819647710.2091.152.050.523.5
9.03-46.7918.50.03290334870.9990.0070.03387.799.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7z4x

7z4x


Resolution: 1.68→45.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 2977 5.09 %
Rwork0.1553 55493 -
obs0.1563 58470 90.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.3 Å2 / Biso mean: 35.3703 Å2 / Biso min: 20.86 Å2
Refinement stepCycle: final / Resolution: 1.68→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 144 331 3607
Biso mean--43.15 37.71 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.710.3948300.382559562520
1.71-1.740.2912790.32131411149049
1.74-1.770.3071020.27341939204167
1.77-1.80.23241010.25712255235677
1.8-1.840.26791200.24112509262987
1.84-1.880.25571500.22732755290596
1.88-1.920.2331550.19828983053100
1.92-1.970.2261480.172529103058100
1.97-2.020.20131520.165729253077100
2.02-2.080.19861410.160529243065100
2.08-2.150.17331810.150228543035100
2.15-2.230.1751590.150429273086100
2.23-2.320.17861930.146628643057100
2.32-2.420.18331460.152329313077100
2.42-2.550.20021730.150828993072100
2.55-2.710.17981660.159129053071100
2.71-2.920.17821440.163229653109100
2.92-3.210.1881530.168429503103100
3.21-3.680.1571640.143529543118100
3.68-4.630.12131740.122829813155100
4.63-45.840.17641460.150431423288100

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