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- PDB-5xkc: Crystal structure of dibenzothiophene sulfone monooxygenase BdsA ... -

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Basic information

Entry
Database: PDB / ID: 5xkc
TitleCrystal structure of dibenzothiophene sulfone monooxygenase BdsA at 2.2 angstrome
ComponentsDibenzothiophene desulfurization enzyme A
KeywordsOXIDOREDUCTASE / dibenzothiophene desulfurization enzyme / monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dibenzothiophene desulfurization enzyme A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.209 Å
AuthorsGu, L. / Su, T. / Liu, S. / Su, J.
CitationJournal: Front Microbiol / Year: 2018
Title: Structural and Biochemical Characterization of BdsA fromBacillus subtilisWU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway.
Authors: Su, T. / Su, J. / Liu, S. / Zhang, C. / He, J. / Huang, Y. / Xu, S. / Gu, L.
History
DepositionMay 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 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: Dibenzothiophene desulfurization enzyme A
B: Dibenzothiophene desulfurization enzyme A
C: Dibenzothiophene desulfurization enzyme A
D: Dibenzothiophene desulfurization enzyme A


Theoretical massNumber of molelcules
Total (without water)198,8394
Polymers198,8394
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16790 Å2
ΔGint-66 kcal/mol
Surface area59900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.494, 174.574, 85.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Dibenzothiophene desulfurization enzyme A


Mass: 49709.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bdsA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GRC7, EC: 1.14.14.22
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium citrate pH 5.5, 35% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 98498 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rsym value: 0.094 / Net I/σ(I): 33.89
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.72 / Rsym value: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b9n

3b9n


Resolution: 2.209→44.883 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.213 4738 4.99 %
Rwork0.1747 --
obs0.1766 94927 95.08 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 40.659 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.328 Å20 Å2-0 Å2
2--1.3956 Å20 Å2
3----9.7236 Å2
Refinement stepCycle: LAST / Resolution: 2.209→44.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13820 0 0 446 14266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714156
X-RAY DIFFRACTIONf_angle_d1.0319241
X-RAY DIFFRACTIONf_dihedral_angle_d15.3795067
X-RAY DIFFRACTIONf_chiral_restr0.0712109
X-RAY DIFFRACTIONf_plane_restr0.0052539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2088-2.23390.28511030.22751719X-RAY DIFFRACTION55
2.2339-2.26020.26881400.20732884X-RAY DIFFRACTION92
2.2602-2.28780.26191630.20142814X-RAY DIFFRACTION91
2.2878-2.31670.27371450.20222901X-RAY DIFFRACTION92
2.3167-2.34720.28781290.20932874X-RAY DIFFRACTION92
2.3472-2.37930.26611590.20962904X-RAY DIFFRACTION92
2.3793-2.41330.26951510.20112895X-RAY DIFFRACTION93
2.4133-2.44940.25141390.19722934X-RAY DIFFRACTION93
2.4494-2.48760.23981350.18752923X-RAY DIFFRACTION93
2.4876-2.52840.26281560.17622970X-RAY DIFFRACTION95
2.5284-2.5720.25241600.18952947X-RAY DIFFRACTION94
2.572-2.61880.24591430.19272986X-RAY DIFFRACTION95
2.6188-2.66910.24421450.18743064X-RAY DIFFRACTION96
2.6691-2.72360.24391700.18352958X-RAY DIFFRACTION96
2.7236-2.78280.24721420.18473047X-RAY DIFFRACTION96
2.7828-2.84750.21011500.18753046X-RAY DIFFRACTION96
2.8475-2.91870.23751680.19073069X-RAY DIFFRACTION97
2.9187-2.99760.25231680.19423069X-RAY DIFFRACTION98
2.9976-3.08580.22521700.19123107X-RAY DIFFRACTION98
3.0858-3.18540.25961870.18713079X-RAY DIFFRACTION99
3.1854-3.29920.23581800.18983129X-RAY DIFFRACTION99
3.2992-3.43130.19651650.17233167X-RAY DIFFRACTION100
3.4313-3.58740.20121390.16933166X-RAY DIFFRACTION100
3.5874-3.77640.18991790.1553150X-RAY DIFFRACTION100
3.7764-4.01290.19151650.15413172X-RAY DIFFRACTION100
4.0129-4.32250.1671700.15113185X-RAY DIFFRACTION100
4.3225-4.7570.19131740.14883210X-RAY DIFFRACTION100
4.757-5.44440.17231680.15953226X-RAY DIFFRACTION100
5.4444-6.85540.21911810.18693248X-RAY DIFFRACTION100
6.8554-44.89240.1741940.16313346X-RAY DIFFRACTION98

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