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- PDB-7z4x: Crystal structure of Variovorax paradoxus indole monooxygenase (V... -

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Basic information

Entry
Database: PDB / ID: 7z4x
TitleCrystal structure of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with FAD
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 / Putative dehydrogenase/oxygenase subunit (Flavoprotein)
Function and homology information
Biological speciesVariovorax paradoxus EPS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 6, 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 1.2May 1, 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)48,1102
Polymers47,3251
Non-polymers7861
Water2,756153
1
A: Putative dehydrogenase/oxygenase subunit (Flavoprotein)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,2204
Polymers94,6492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5510 Å2
ΔGint-27 kcal/mol
Surface area30040 Å2
Unit cell
Length a, b, c (Å)94.512, 94.512, 111.253
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: 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 (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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Na-acetate pH 5, 1400 mM Na-malonate, 1 mM FAD

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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: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→47.26 Å / Num. obs: 36562 / % possible obs: 99.7 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.039 / Rrim(I) all: 0.131 / Net I/σ(I): 13.7 / Num. measured all: 401701 / 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
2.05-2.110.82.1912949327270.70.6912.2991.496.9
8.93-47.2690.03546445180.9990.0120.0375099.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: robetta_prediction

Resolution: 2.05→38.41 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1736 4.76 %
Rwork0.1744 34726 -
obs0.1762 36462 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.81 Å2 / Biso mean: 47.7329 Å2 / Biso min: 26.44 Å2
Refinement stepCycle: final / Resolution: 2.05→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 86 153 3376
Biso mean--71.05 42.62 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.110.34681390.28912774291397
2.11-2.180.27621210.240728742995100
2.18-2.260.25171240.241928722996100
2.26-2.350.27381810.224228122993100
2.35-2.450.24031490.206928723021100
2.45-2.580.22991460.187828853031100
2.58-2.740.28311510.195428863037100
2.74-2.950.29171490.187428933042100
2.96-3.250.23211450.199229053050100
3.25-3.720.22191210.156929413062100
3.72-4.690.1591460.13329563102100
4.69-38.410.16051640.151630563220100
Refinement TLS params.Method: refined / Origin x: 17.9428 Å / Origin y: 56.3788 Å / Origin z: 12.7614 Å
111213212223313233
T0.3017 Å20.0772 Å2-0.0055 Å2-0.3661 Å2-0.0338 Å2--0.309 Å2
L0.6796 °2-0.0654 °20.2203 °2-0.3254 °2-0.1875 °2--0.6663 °2
S-0.0254 Å °-0.2365 Å °0.0236 Å °-0.0053 Å °-0.014 Å °-0.0295 Å °-0.1513 Å °-0.1046 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 412
2X-RAY DIFFRACTION1allA500
3X-RAY DIFFRACTION1allS1 - 175

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