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- PDB-7z94: Crystal structure of Variovorax paradoxus indole monooxygenase (V... -

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Basic information

Entry
Database: PDB / ID: 7z94
TitleCrystal structure of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with indole
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 / INDOLE / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 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 19, 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)49,31914
Polymers47,3251
Non-polymers1,99513
Water4,756264
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)98,63928
Polymers94,6492
Non-polymers3,99026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11700 Å2
ΔGint-54 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.938, 93.938, 110.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-791-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47324.570 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 BL21(DE3) (bacteria) / References: UniProt: E6V140

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Non-polymers , 6 types, 277 molecules

#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-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: A solution of 13.6 mg/mL protein was supplemented with 6.2 mM FAD, 18.4 mM indole and 6.2 % (v/v) DMSO and mixed in a 1:1 ratio with 100 mM Tris/HCl (pH 8.5) and 2 M ammonium sulfate. ...Details: A solution of 13.6 mg/mL protein was supplemented with 6.2 mM FAD, 18.4 mM indole and 6.2 % (v/v) DMSO and mixed in a 1:1 ratio with 100 mM Tris/HCl (pH 8.5) and 2 M ammonium sulfate. Crystals were cryo-protected by swiping them through 50 mM Tris/HCl (pH 8.5), 2.3 M ammonium sulfate, 12 % (v/v) ethylene glycol, 3 mM FAD and 10 mM indole.

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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: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.74→46.97 Å / Num. obs: 58636 / % possible obs: 99.9 % / Redundancy: 15.5 % / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.024 / Rrim(I) all: 0.096 / Net I/σ(I): 18.3 / Num. measured all: 907355
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
1.74-1.7715.53.314904831700.4080.8613.4210.998.2
9.03-46.9713.70.022670148810.0060.02383.499.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7Z4X

7z4x


Resolution: 1.74→40.68 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 2944 5.03 %
Rwork0.1615 55606 -
obs0.1628 58550 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.61 Å2 / Biso mean: 37.7677 Å2 / Biso min: 20.77 Å2
Refinement stepCycle: final / Resolution: 1.74→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 221 264 3639
Biso mean--50.2 41.79 -
Num. residues----413
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 (%)
1.74-1.770.31621380.31392553269198
1.77-1.80.33471320.291726462778100
1.8-1.830.27161400.265926052745100
1.83-1.870.27831320.243926232755100
1.87-1.90.271520.23425872739100
1.9-1.940.24571360.214826532789100
1.94-1.990.21721350.189626422777100
1.99-2.040.25661030.175126512754100
2.04-2.090.21021690.162126192788100
2.1-2.160.18221190.155426022721100
2.16-2.230.19211290.156826752804100
2.23-2.310.18591630.151926132776100
2.31-2.40.21011450.145426342779100
2.4-2.510.18321520.148526392791100
2.51-2.640.17341320.147826602792100
2.64-2.80.18271400.150326492789100
2.81-3.020.17861540.17326612815100
3.02-3.320.18821540.162626342788100
3.33-3.810.16721430.147226852828100
3.81-4.790.13141290.133627422871100
4.8-40.680.20831470.165128332980100
Refinement TLS params.Method: refined / Origin x: 18.2678 Å / Origin y: 56.2811 Å / Origin z: 12.792 Å
111213212223313233
T0.2625 Å20.0163 Å20.0131 Å2-0.2221 Å2-0.0187 Å2--0.2427 Å2
L0.5008 °2-0.0712 °2-0.0465 °2-0.3415 °2-0.2388 °2--0.5465 °2
S-0.0293 Å °-0.0452 Å °0.0267 Å °0.0252 Å °0.0137 Å °-0.0159 Å °-0.0094 Å °0.0108 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 412
2X-RAY DIFFRACTION1allA501 - 510
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allE1 - 267

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