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- PDB-8t0u: Crystal structure of dimethylsulfone monooxygenase SfnG from Pseu... -

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Basic information

Entry
Database: PDB / ID: 8t0u
TitleCrystal structure of dimethylsulfone monooxygenase SfnG from Pseudomonas fluorescens
ComponentsFMNH(2)-dependent dimethylsulfone monooxygenase
KeywordsFLAVOPROTEIN / two-component / sulfate bound / FMN-dependent / unliganded
Function / homologydimethylsulfone monooxygenase / FMNH(2)-dependent dimethylsulfone monooxygenase SfnG / alkanesulfonate monooxygenase activity / : / alkanesulfonate catabolic process / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / FMNH(2)-dependent dimethylsulfone monooxygenase
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGonzalez, R. / Soule, J. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1807480 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural, biophysical, and biochemical insights into C-S bond cleavage by dimethylsulfone monooxygenase.
Authors: Gonzalez, R. / Soule, J. / Phan, N. / Wicht, D.K. / Dowling, D.P.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMNH(2)-dependent dimethylsulfone monooxygenase
B: FMNH(2)-dependent dimethylsulfone monooxygenase
C: FMNH(2)-dependent dimethylsulfone monooxygenase
D: FMNH(2)-dependent dimethylsulfone monooxygenase
E: FMNH(2)-dependent dimethylsulfone monooxygenase
F: FMNH(2)-dependent dimethylsulfone monooxygenase
G: FMNH(2)-dependent dimethylsulfone monooxygenase
H: FMNH(2)-dependent dimethylsulfone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,68828
Polymers342,7678
Non-polymers1,92120
Water1,24369
1
A: FMNH(2)-dependent dimethylsulfone monooxygenase
B: FMNH(2)-dependent dimethylsulfone monooxygenase
C: FMNH(2)-dependent dimethylsulfone monooxygenase
D: FMNH(2)-dependent dimethylsulfone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,34414
Polymers171,3834
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: FMNH(2)-dependent dimethylsulfone monooxygenase
F: FMNH(2)-dependent dimethylsulfone monooxygenase
G: FMNH(2)-dependent dimethylsulfone monooxygenase
H: FMNH(2)-dependent dimethylsulfone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,34414
Polymers171,3834
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.785, 94.506, 102.056
Angle α, β, γ (deg.)103.827, 100.585, 96.521
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 17 or resid 19...
d_2ens_1(chain "B" and (resid 7 through 17 or resid 19...
d_3ens_1(chain "C" and (resid 7 through 16 or resid 31...
d_4ens_1(chain "D" and (resid 7 through 17 or resid 19...
d_5ens_1(chain "E" and (resid 7 through 17 or resid 19...
d_6ens_1(chain "F" and (resid 7 through 17 or resid 19...
d_7ens_1(chain "G" and (resid 7 through 16 or resid 31...
d_8ens_1(chain "H" and (resid 7 through 17 or resid 19...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSGLYGLYAA7 - 1730 - 40
d_12LEULEULEULEUAA1942
d_13GLNGLNGLYGLYAA40 - 5963 - 82
d_14SERSERPHEPHEAA68 - 12291 - 145
d_15GLYGLYGLUGLUAA124 - 125147 - 148
d_16GLNGLNTYRTYRAA127 - 140150 - 163
d_17ARGARGSERSERAA142 - 143165 - 166
d_18GLUGLUILEILEAA145 - 256168 - 279
d_19GLYGLYGLNGLNAA299 - 334322 - 357
d_110GLUGLUVALVALAA336 - 337359 - 360
d_111TYRTYRGLUGLUAA339 - 352362 - 375
d_21LYSLYSGLYGLYBB7 - 1730 - 40
d_22LEULEULEULEUBB1942
d_23GLNGLNGLYGLYBB40 - 5963 - 82
d_24SERSERPHEPHEBB68 - 12291 - 145
d_25GLYGLYGLUGLUBB124 - 125147 - 148
d_26GLNGLNTYRTYRBB127 - 140150 - 163
d_27ARGARGSERSERBB142 - 143165 - 166
d_28GLUGLUILEILEBB145 - 256168 - 279
d_29GLYGLYGLNGLNBB299 - 334322 - 357
d_210GLUGLUVALVALBB336 - 337359 - 360
d_211TYRTYRGLUGLUBB339 - 352362 - 375
d_31LYSLYSSERSERCC7 - 1630 - 39
d_32GLYGLYGLYGLYCC3154
d_33LEULEULEULEUCC3861
d_34GLNGLNGLYGLYCC40 - 5963 - 82
d_35SERSERPHEPHECC68 - 12291 - 145
d_36GLYGLYGLUGLUCC124 - 125147 - 148
d_37GLNGLNARGARGCC127 - 141150 - 164
d_38SERSERGLUGLUCC143 - 144166 - 167
d_39PHEPHEILEILECC146 - 256169 - 279
d_310GLYGLYGLUGLUCC299 - 335322 - 358
d_311VALVALVALVALCC337360
d_312TYRTYRGLUGLUCC339 - 352362 - 375
d_41LYSLYSGLYGLYDD7 - 1730 - 40
d_42LEULEULEULEUDD1942
d_43GLNGLNGLYGLYDD40 - 5963 - 82
d_44SERSERPHEPHEDD68 - 12291 - 145
d_45GLYGLYGLUGLUDD124 - 125147 - 148
d_46GLNGLNTYRTYRDD127 - 140150 - 163
d_47ARGARGSERSERDD142 - 143165 - 166
d_48GLUGLUILEILEDD145 - 256168 - 279
d_49GLYGLYGLNGLNDD299 - 334322 - 357
d_410GLUGLUVALVALDD336 - 337359 - 360
d_411TYRTYRGLUGLUDD339 - 352362 - 375
d_51LYSLYSGLYGLYEE7 - 1730 - 40
d_52LEULEULEULEUEE1942
d_53GLNGLNGLYGLYEE40 - 5963 - 82
d_54SERSERPHEPHEEE68 - 12291 - 145
d_55GLYGLYGLUGLUEE124 - 125147 - 148
d_56GLNGLNTYRTYREE127 - 140150 - 163
d_57ARGARGSERSEREE142 - 143165 - 166
d_58GLUGLUILEILEEE145 - 256168 - 279
d_59GLYGLYGLUGLUEE299 - 335322 - 358
d_510VALVALVALVALEE337360
d_511TYRTYRGLUGLUEE339 - 352362 - 375
d_61LYSLYSGLYGLYFF7 - 1730 - 40
d_62LEULEULEULEUFF1942
d_63GLNGLNGLYGLYFF40 - 5963 - 82
d_64SERSERPHEPHEFF68 - 12291 - 145
d_65GLYGLYGLUGLUFF124 - 125147 - 148
d_66GLNGLNTYRTYRFF127 - 140150 - 163
d_67ARGARGGLUGLUFF142 - 144165 - 167
d_68PHEPHEILEILEFF146 - 256169 - 279
d_69GLYGLYGLNGLNFF299 - 334322 - 357
d_610GLUGLUVALVALFF336 - 337359 - 360
d_611TYRTYRGLUGLUFF339 - 352362 - 375
d_71LYSLYSSERSERGG7 - 1630 - 39
d_72GLYGLYGLYGLYGG3154
d_73LEULEULEULEUGG3861
d_74GLNGLNGLYGLYGG40 - 5963 - 82
d_75SERSERPHEPHEGG68 - 12291 - 145
d_76GLYGLYGLUGLUGG124 - 125147 - 148
d_77GLNGLNARGARGGG127 - 141150 - 164
d_78SERSERGLUGLUGG143 - 144166 - 167
d_79PHEPHEILEILEGG146 - 256169 - 279
d_710GLYGLYGLUGLUGG299 - 335322 - 358
d_711VALVALVALVALGG337360
d_712TYRTYRGLUGLUGG339 - 352362 - 375
d_81LYSLYSGLYGLYHH7 - 1730 - 40
d_82LEULEULEULEUHH1942
d_83GLNGLNGLYGLYHH40 - 5963 - 82
d_84SERSERPHEPHEHH68 - 12291 - 145
d_85GLYGLYGLUGLUHH124 - 125147 - 148
d_86GLNGLNTYRTYRHH127 - 140150 - 163
d_87ARGARGSERSERHH142 - 143165 - 166
d_88GLUGLUILEILEHH145 - 256168 - 279
d_89GLYGLYGLNGLNHH299 - 334322 - 357
d_810GLUGLUVALVALHH336 - 337359 - 360
d_811TYRTYRGLUGLUHH339 - 352362 - 375

NCS oper:
IDCodeMatrixVector
1given(-0.995313859547, -0.00729378123035, -0.0964215834188), (0.0083895290497, -0.999904703017, -0.0109636073765), (-0.0963324285791, -0.0117211620476, 0.995280200529)89.0217872929, 13.7575624372, 4.29767606472
2given(-0.914353798854, -0.404847994764, 0.00743180037837), (-0.404631169555, 0.914244790812, 0.0207383484587), (-0.0151903635705, 0.0159550496162, -0.999757315175)95.0309886887, 21.3723492242, -129.973835073
3given(0.903009389304, 0.422578726735, 0.077467816152), (0.419617516599, -0.906211266198, 0.0519834663992), (0.092169314807, -0.0144347056171, -0.99563871795)6.08405451337, -2.40034836952, -134.508637792
4given(-0.861537070683, -0.38684486103, 0.328793140642), (-0.392052448604, 0.91839999395, 0.0532571934767), (-0.322565889986, -0.0830211094121, -0.942899115499)122.921329484, -24.5668956212, -111.489183058
5given(0.824203674896, 0.382061943139, 0.417991595482), (0.379427591754, -0.920512787545, 0.0932250534082), (0.420384353782, 0.0817611128357, -0.903654865268)42.5129953247, -44.81648733, -145.714336636
6given(0.936675566395, 0.00959688850887, -0.350066826547), (-0.0463438486803, 0.994229559794, -0.0967462150244), (0.347118324217, 0.106843259792, 0.931715292796)-10.4327992451, -51.4677583952, -22.7325087703
7given(-0.906295276824, -0.00974737630164, -0.422532673129), (0.0500797886602, -0.99516764717, -0.0844592729898), (-0.419667589854, -0.097705387167, 0.902403884823)73.4260141294, -40.081529947, 13.7965165909

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Components

#1: Protein
FMNH(2)-dependent dimethylsulfone monooxygenase


Mass: 42845.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: sfnG, Pfl01_2879 / Plasmid: pET28-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): NEB-T7 Express / References: UniProt: Q3KC85, dimethylsulfone monooxygenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.52 % / Description: Seeded triclinic crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M Bis-Tris (pH 5.5), 0.1 M (NH4)2SO4, 30% (w/v) PEG 3350, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→96.7 Å / Num. obs: 92082 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 65.04 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Rsym value: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 14485 / CC1/2: 0.79 / Rpim(I) all: 0.425 / Rrim(I) all: 0.702 / Rsym value: 0.679 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSJan 31, 2020data reduction
XDSJan 31, 2020data scaling
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→72.66 Å / SU ML: 0.3744 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.3926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Refinement of unliganded structure contained an unordered lid region.
RfactorNum. reflection% reflection
Rfree0.236 4598 5 %
Rwork0.2005 87377 -
obs0.2023 91975 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19528 0 100 69 19697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001920098
X-RAY DIFFRACTIONf_angle_d0.437127293
X-RAY DIFFRACTIONf_chiral_restr0.0562974
X-RAY DIFFRACTIONf_plane_restr0.00343563
X-RAY DIFFRACTIONf_dihedral_angle_d10.93226981
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.52950089237
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.48260509044
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.543955225884
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.470576599237
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.596897970685
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS1.53795489488
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.462964770101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.3661460.32272818X-RAY DIFFRACTION92.83
2.63-2.660.31451520.28462886X-RAY DIFFRACTION95.65
2.66-2.690.33031540.27742913X-RAY DIFFRACTION94.14
2.69-2.730.31451500.25912855X-RAY DIFFRACTION94.71
2.73-2.760.28921510.25232875X-RAY DIFFRACTION93.57
2.76-2.80.35421450.25762752X-RAY DIFFRACTION91.94
2.8-2.840.3251450.25572756X-RAY DIFFRACTION89.93
2.84-2.880.31251550.27622931X-RAY DIFFRACTION97.44
2.88-2.930.38461570.3112989X-RAY DIFFRACTION97.49
2.93-2.980.32461570.28772987X-RAY DIFFRACTION97.43
2.98-3.030.32081540.2832923X-RAY DIFFRACTION97.44
3.03-3.080.33511570.26052985X-RAY DIFFRACTION97.37
3.08-3.140.31641560.23952964X-RAY DIFFRACTION97.23
3.14-3.210.25061560.21752954X-RAY DIFFRACTION97.55
3.21-3.280.27671560.21262968X-RAY DIFFRACTION97.32
3.28-3.350.27581540.22032935X-RAY DIFFRACTION97.14
3.35-3.440.26911550.2242943X-RAY DIFFRACTION96.54
3.44-3.530.25531550.23822941X-RAY DIFFRACTION96.24
3.53-3.630.24241540.2142927X-RAY DIFFRACTION96.28
3.63-3.750.23671520.19312876X-RAY DIFFRACTION95.37
3.75-3.880.26381540.18792919X-RAY DIFFRACTION95.05
3.88-4.040.20811480.19092814X-RAY DIFFRACTION92.56
4.04-4.220.19461470.16722798X-RAY DIFFRACTION91.86
4.22-4.450.21321560.16032969X-RAY DIFFRACTION97.66
4.45-4.720.17361570.15822983X-RAY DIFFRACTION97.85
4.72-5.090.19511570.15952978X-RAY DIFFRACTION97.97
5.09-5.60.22341560.18762967X-RAY DIFFRACTION97.72
5.6-6.410.23131560.20342970X-RAY DIFFRACTION97.5
6.41-8.070.2021510.17932862X-RAY DIFFRACTION94.1
8.08-72.660.17181550.17092939X-RAY DIFFRACTION96.96

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