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- PDB-5xb8: Crystal structure of dibenzothiophene monooxygenase (TdsC) from P... -

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Basic information

Entry
Database: PDB / ID: 5xb8
TitleCrystal structure of dibenzothiophene monooxygenase (TdsC) from Paenibacillus sp. A11-2
ComponentsThermophilic dibenzothiophene desulfurization enzyme C
KeywordsOXIDOREDUCTASE / Monooxygenase / FMN binding protein / tetramer
Function / homology
Function and homology information


dibenzothiophene monooxygenase / 3-methylbutanoyl-CoA dehydrogenase activity / L-leucine catabolic process / 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 monooxygenase
Similarity search - Component
Biological speciesPaenibacillus sp. A11-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 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 16, 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)183,83310
Polymers183,2574
Non-polymers5766
Water41,7952320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Homologue proteins also form same tetrameric assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-151 kcal/mol
Surface area54060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.970, 100.970, 423.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2320 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.3M Ammonium sulfate, 0.1M Tris-HCl, 12% 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: Nov 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.795→49.109 Å / Num. obs: 390677 / % possible obs: 99.8 % / Redundancy: 14 % / Net I/σ(I): 20.31
Reflection shellResolution: 1.8→1.86 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NF4

3nf4


Resolution: 1.795→49.109 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3
RfactorNum. reflection% reflection
Rfree0.1781 19524 5 %
Rwork0.1513 --
obs0.1527 390677 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.795→49.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11999 0 30 2320 14349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712317
X-RAY DIFFRACTIONf_angle_d0.83116765
X-RAY DIFFRACTIONf_dihedral_angle_d17.0487199
X-RAY DIFFRACTIONf_chiral_restr0.051829
X-RAY DIFFRACTIONf_plane_restr0.0062189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7946-1.8150.30696220.275111834X-RAY DIFFRACTION96
1.815-1.83630.28236480.259912501X-RAY DIFFRACTION100
1.8363-1.85870.27656460.243312274X-RAY DIFFRACTION100
1.8587-1.88230.25476570.227512432X-RAY DIFFRACTION100
1.8823-1.9070.23726620.210412458X-RAY DIFFRACTION100
1.907-1.93310.23626380.199112311X-RAY DIFFRACTION100
1.9331-1.96080.22576520.193212364X-RAY DIFFRACTION100
1.9608-1.990.22076530.190412398X-RAY DIFFRACTION100
1.99-2.02110.20676560.182712449X-RAY DIFFRACTION100
2.0211-2.05430.20836430.166812370X-RAY DIFFRACTION100
2.0543-2.08970.20076550.164112381X-RAY DIFFRACTION100
2.0897-2.12770.19546580.15712353X-RAY DIFFRACTION100
2.1277-2.16860.18426510.154912389X-RAY DIFFRACTION100
2.1686-2.21290.18176570.144512393X-RAY DIFFRACTION100
2.2129-2.2610.16386500.141212411X-RAY DIFFRACTION100
2.261-2.31360.17046450.136712364X-RAY DIFFRACTION100
2.3136-2.37150.1536460.128812367X-RAY DIFFRACTION100
2.3715-2.43560.16826510.134612403X-RAY DIFFRACTION100
2.4356-2.50720.1696520.13412438X-RAY DIFFRACTION100
2.5072-2.58820.15766550.132812415X-RAY DIFFRACTION100
2.5882-2.68070.16346410.130612339X-RAY DIFFRACTION100
2.6807-2.7880.16736520.132812419X-RAY DIFFRACTION100
2.788-2.91480.1686450.136612393X-RAY DIFFRACTION100
2.9148-3.06850.18596500.141412384X-RAY DIFFRACTION100
3.0685-3.26070.17596480.139812416X-RAY DIFFRACTION100
3.2607-3.51240.15886590.138512367X-RAY DIFFRACTION100
3.5124-3.86580.14656630.13112382X-RAY DIFFRACTION100
3.8658-4.42480.13816600.120712374X-RAY DIFFRACTION100
4.4248-5.57360.15546460.134612387X-RAY DIFFRACTION100
5.5736-49.12740.19166630.189512363X-RAY DIFFRACTION100

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