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- PDB-5xdb: Crystal structure of FMN-bound TdsC from Paenibacillus sp. A11-2 -

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Basic information

Entry
Database: PDB / ID: 5xdb
TitleCrystal structure of FMN-bound 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
FLAVIN MONONUCLEOTIDE / Dibenzothiophene monooxygenase
Similarity search - Component
Biological speciesPaenibacillus sp. A11-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.811 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 1.2Nov 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

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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)185,74715
Polymers183,2574
Non-polymers2,49011
Water29,4181633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21910 Å2
ΔGint-191 kcal/mol
Surface area52240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.820, 100.820, 424.400
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1633 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.811→35.51 Å / Num. obs: 527346 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XB8

5xb8


Resolution: 1.811→35.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 24
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2117 18958 5 %
Rwork0.1898 --
obs0.1909 527346 92.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.811→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12441 0 161 1633 14235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612911
X-RAY DIFFRACTIONf_angle_d0.80517589
X-RAY DIFFRACTIONf_dihedral_angle_d16.6817517
X-RAY DIFFRACTIONf_chiral_restr0.0481903
X-RAY DIFFRACTIONf_plane_restr0.0052281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.811-1.84040.29279390.269718077X-RAY DIFFRACTION100
1.8404-1.87390.28889530.27218145X-RAY DIFFRACTION100
1.8739-1.90990.29579510.269618034X-RAY DIFFRACTION100
1.9099-1.94890.39420.274517833X-RAY DIFFRACTION99
1.9489-1.99130.25769580.217918078X-RAY DIFFRACTION100
1.9913-2.03760.2279540.205218160X-RAY DIFFRACTION100
2.0376-2.08860.24529400.21117914X-RAY DIFFRACTION99
2.0886-2.14510.21759540.186118164X-RAY DIFFRACTION100
2.1451-2.20820.21759620.18818017X-RAY DIFFRACTION100
2.2082-2.27940.23579370.197917925X-RAY DIFFRACTION99
2.2794-2.36090.18519500.165818103X-RAY DIFFRACTION100
2.3609-2.45540.19929460.166618186X-RAY DIFFRACTION100
2.4554-2.56720.20439470.166618072X-RAY DIFFRACTION100
2.5672-2.70250.19559500.167918060X-RAY DIFFRACTION100
2.7025-2.87180.19379620.166418135X-RAY DIFFRACTION100
2.8718-3.09350.18149540.158318086X-RAY DIFFRACTION100
3.0935-3.40470.17869500.153118127X-RAY DIFFRACTION100
3.4047-3.89720.15899550.144718013X-RAY DIFFRACTION99
3.8972-4.90930.14329470.136718069X-RAY DIFFRACTION100
4.7506-4.90930.1859550.173618032X-RAY DIFFRACTION100

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