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- PDB-7z97: Crystal structure of the F191M variant of Variovorax paradoxus in... -

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Basic information

Entry
Database: PDB / ID: 7z97
TitleCrystal structure of the F191M variant of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with 6-bromoindole
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 / 6-bromo-1H-indole / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 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)48,3524
Polymers47,3091
Non-polymers1,0443
Water4,450247
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,7058
Polymers94,6172
Non-polymers2,0876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5820 Å2
ΔGint-18 kcal/mol
Surface area30120 Å2
Unit cell
Length a, b, c (Å)95.863, 95.863, 111.522
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 / Mutation: F191M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus EPS (bacteria) / Strain: EPS / Gene: Varpa_4903 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FK1 / 6-bromo-1H-indole


Mass: 196.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6BrN / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.46→83.02 Å / Num. obs: 99972 / % possible obs: 97.6 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Net I/σ(I): 12.8 / Num. measured all: 726615 / 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
1.46-1.491.91.679551728350.4151.3352.1610.356.1
8.01-83.025.50.04437976860.9950.0210.04939.696.9

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Processing

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

7z4x


Resolution: 1.46→83.02 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 4917 5.01 %
Rwork0.1701 93262 -
obs0.172 98179 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.1 Å2 / Biso mean: 48.9244 Å2 / Biso min: 31.3 Å2
Refinement stepCycle: final / Resolution: 1.46→83.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 103 247 3488
Biso mean--46.63 51.11 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.480.6924460.63391108115434
1.48-1.50.57251230.60682289241271
1.5-1.520.52551700.52432989315994
1.52-1.530.5221850.47043106329198
1.54-1.560.45472000.43783116331699
1.56-1.580.47151640.4163182334699
1.58-1.60.43211540.38323215336999
1.6-1.620.41721470.36043146329399
1.62-1.650.3561690.33293188335799
1.65-1.680.40641830.313159334299
1.68-1.70.33441510.29243189334099
1.7-1.740.26951870.26243173336099
1.74-1.770.31271590.2453197335699
1.77-1.80.28681760.24963197337399
1.8-1.840.28041550.22523207336299
1.84-1.890.2532240.21853151337599
1.89-1.930.2251410.20143200334199
1.93-1.990.28151700.19113210338099
1.99-2.040.23591420.18623248339099
2.04-2.110.21691340.169832433377100
2.11-2.190.22461950.168832003395100
2.19-2.270.21111320.167632613393100
2.27-2.380.22061520.173332593411100
2.38-2.50.17931490.169432683417100
2.5-2.660.23081610.163632643425100
2.66-2.860.21571770.179732383415100
2.86-3.150.22021740.173832603434100
3.15-3.610.18932050.149932763481100
3.61-4.550.15732000.120533043504100
4.55-83.020.16911920.14013419361199

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