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- PDB-7z98: Crystal structure of F191M variant Variovorax paradoxus indole mo... -

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Basic information

Entry
Database: PDB / ID: 7z98
TitleCrystal structure of F191M variant Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with methyl phenyl sulfide
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 / (methylsulfanyl)benzene / FLAVIN-ADENINE DINUCLEOTIDE / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 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)48,3425
Polymers47,3091
Non-polymers1,0344
Water6,612367
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,68510
Polymers94,6172
Non-polymers2,0688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6290 Å2
ΔGint-12 kcal/mol
Surface area30260 Å2
Unit cell
Length a, b, c (Å)94.485, 94.485, 111.009
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-16R / (methylsulfanyl)benzene / methyl phenyl sulfide


Mass: 124.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
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 methyl phenyl sulfide, 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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→47.24 Å / Num. obs: 59530 / % possible obs: 98.2 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 12.4 / Num. measured all: 514810
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
1.73-1.764.12.191082026530.2581.1942.5060.680.7
8.97-47.247.20.03736605060.9990.0140.044199.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7z4x

7z4x


Resolution: 1.73→45.93 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 3017 5.08 %
Rwork0.1844 56417 -
obs0.186 59434 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.52 Å2 / Biso mean: 37.6668 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: final / Resolution: 1.73→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 137 367 3642
Biso mean--41.61 40.83 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.750.4162940.38962063215779
1.75-1.780.44861150.38152331244689
1.78-1.810.35881190.35382422254194
1.81-1.850.38891420.32732513265597
1.85-1.880.31911480.30482525267399
1.88-1.920.33911230.272726152738100
1.92-1.960.2761250.262425792704100
1.96-2.010.29941450.24325872732100
2.01-2.060.24951320.235826232755100
2.06-2.110.2771540.218725542708100
2.11-2.180.2611180.213626342752100
2.18-2.250.23771400.208225992739100
2.25-2.330.18191460.200225702716100
2.33-2.420.241590.18626092768100
2.42-2.530.23651450.19125772722100
2.53-2.660.2471420.187326082750100
2.66-2.830.24131490.193626232772100
2.83-3.050.23351250.19126492774100
3.05-3.350.22181480.18226312779100
3.35-3.840.18291320.146226582790100
3.84-4.840.15691620.126426622824100
4.84-45.930.17141540.156627852939100

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