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- PDB-5xdg: Crystal structure of tertiary complex of TdsC from Paenibacillus ... -

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Basic information

Entry
Database: PDB / ID: 5xdg
TitleCrystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and dibenzothiophene sulfoxide
ComponentsThermophilic dibenzothiophene desulfurization enzyme C
KeywordsOXIDOREDUCTASE / Monooxygenase / FMN binding protein / tetramer
Function / homology
Function and homology information


dibenzothiophene monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
dibenzothiophene 5-oxide / FLAVIN MONONUCLEOTIDE / Dibenzothiophene monooxygenase
Similarity search - Component
Biological speciesPaenibacillus sp. A11-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å
AuthorsHino, T. / Hamamoto, H. / Ohshiro, T. / Nagano, S.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity.
Authors: Hino, T. / Hamamoto, H. / Suzuki, H. / Yagi, H. / Ohshiro, T. / Nagano, S.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermophilic dibenzothiophene desulfurization enzyme C
B: Thermophilic dibenzothiophene desulfurization enzyme C
C: Thermophilic dibenzothiophene desulfurization enzyme C
D: Thermophilic dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,54819
Polymers183,2574
Non-polymers3,29115
Water32,6791814
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21820 Å2
ΔGint-191 kcal/mol
Surface area52010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.830, 100.830, 425.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thermophilic dibenzothiophene desulfurization enzyme C


Mass: 45814.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. A11-2 (bacteria) / Gene: tdsC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LBX2

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Non-polymers , 5 types, 1829 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-83U / dibenzothiophene 5-oxide


Mass: 200.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1814 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.4 M ammonium sulfate, 0.1 M Tris-HCl, 12% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→49.2 Å / Num. obs: 265548 / % possible obs: 99.1 % / Redundancy: 5.1 % / Net I/σ(I): 12.36
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 40906 / CC1/2: 0.513 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.747→47.505 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.2121 10911 5 %
Rwork0.1757 --
obs0.1775 218239 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.747→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12441 0 217 1814 14472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612975
X-RAY DIFFRACTIONf_angle_d0.88117681
X-RAY DIFFRACTIONf_dihedral_angle_d16.7167653
X-RAY DIFFRACTIONf_chiral_restr0.051903
X-RAY DIFFRACTIONf_plane_restr0.0052289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7473-1.76720.36853040.32955766X-RAY DIFFRACTION83
1.7672-1.7880.3633550.3086749X-RAY DIFFRACTION97
1.788-1.80980.3123560.29736758X-RAY DIFFRACTION97
1.8098-1.83270.31343600.27576859X-RAY DIFFRACTION98
1.8327-1.85680.2893520.25416687X-RAY DIFFRACTION98
1.8568-1.88220.28872890.24816859X-RAY DIFFRACTION98
1.8822-1.90910.29483830.23686821X-RAY DIFFRACTION98
1.9091-1.93760.29483460.22986828X-RAY DIFFRACTION98
1.9376-1.96790.27213400.21856835X-RAY DIFFRACTION98
1.9679-2.00010.2683620.21246854X-RAY DIFFRACTION98
2.0001-2.03460.25363720.20596846X-RAY DIFFRACTION98
2.0346-2.07160.24513610.19946852X-RAY DIFFRACTION98
2.0716-2.11150.23883570.19516897X-RAY DIFFRACTION99
2.1115-2.15460.24583560.19416914X-RAY DIFFRACTION99
2.1546-2.20140.22843590.18856927X-RAY DIFFRACTION99
2.2014-2.25260.2233720.18646918X-RAY DIFFRACTION99
2.2526-2.3090.22023600.17546924X-RAY DIFFRACTION99
2.309-2.37140.21173910.17416934X-RAY DIFFRACTION99
2.3714-2.44120.23043840.17436960X-RAY DIFFRACTION100
2.4412-2.520.22133610.17657039X-RAY DIFFRACTION100
2.52-2.610.21963540.17387016X-RAY DIFFRACTION100
2.61-2.71450.20593630.16687056X-RAY DIFFRACTION100
2.7145-2.8380.19973790.17026997X-RAY DIFFRACTION100
2.838-2.98760.21023770.16487044X-RAY DIFFRACTION99
2.9876-3.17480.20993680.16327062X-RAY DIFFRACTION99
3.1748-3.41990.19544140.15196987X-RAY DIFFRACTION99
3.4199-3.76390.16233720.14387072X-RAY DIFFRACTION99
3.7639-4.30820.16613540.13737107X-RAY DIFFRACTION98
4.3082-5.42670.17044100.14417175X-RAY DIFFRACTION99
5.4267-47.5230.18814000.17267585X-RAY DIFFRACTION99

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