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- PDB-23fy: Crystal structure of sulX mutant-S375A in complex with FMN and su... -

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Basic information

Entry
Database: PDB / ID: 23fy
TitleCrystal structure of sulX mutant-S375A in complex with FMN and sulfamethazine
ComponentsSulfonamide monooxygenase
KeywordsOXIDOREDUCTASE / FMN-dependent / Sulfonamide resistance / Sulfonamide degradation
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Sulfonamide monooxygenase
Similarity search - Component
Biological speciesMicrobacterium sp. CJ77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsHu, Y.M. / Liu, W.H. / Zhang, Q.S. / Gao, Z.D. / Zhang, H.L. / Li, H. / Dai, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2100400 China
CitationJournal: J Hazard Mater / Year: 2026
Title: Structural insights into sulfonamide degradation by a two-component flavin-dependent monooxygenase.
Authors: Hu, Y. / Liu, W. / Zhang, Q. / Gao, Z. / Zhang, H. / Li, H. / Dai, L.
History
DepositionFeb 5, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfonamide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,27310
Polymers45,9481
Non-polymers1,3259
Water1,40578
1
A: Sulfonamide monooxygenase
hetero molecules

A: Sulfonamide monooxygenase
hetero molecules

A: Sulfonamide monooxygenase
hetero molecules

A: Sulfonamide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,09440
Polymers183,7934
Non-polymers5,30136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area12760 Å2
ΔGint-71 kcal/mol
Surface area51700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.602, 133.602, 139.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfonamide monooxygenase


Mass: 45948.262 Da / Num. of mol.: 1 / Mutation: S375A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. CJ77 (bacteria) / Gene: sulX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482P9Z9

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Non-polymers , 6 types, 87 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1E1F / Sulfamethazine / 4-azanyl-~{N}-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide


Mass: 278.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 24%PEG 500, 1.2 mM ZnSO4, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→20 Å / Num. obs: 22409 / % possible obs: 99.9 % / Redundancy: 31 % / CC1/2: 0.991 / Net I/σ(I): 31.1
Reflection shellResolution: 2.63→2.72 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2178 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→19.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.933 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24022 1100 4.9 %RANDOM
Rwork0.18034 ---
obs0.18334 21279 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.162 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.29 Å20 Å2
2--2.57 Å2-0 Å2
3----8.35 Å2
Refinement stepCycle: 1 / Resolution: 2.62→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 75 78 3169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172833
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6664295
X-RAY DIFFRACTIONr_angle_other_deg1.2991.5876524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49421.329173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18515471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4911528
X-RAY DIFFRACTIONr_chiral_restr0.0620.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.088.0141575
X-RAY DIFFRACTIONr_mcbond_other6.0718.0131574
X-RAY DIFFRACTIONr_mcangle_it8.24312.0171967
X-RAY DIFFRACTIONr_mcangle_other8.24212.0171968
X-RAY DIFFRACTIONr_scbond_it6.7288.5481572
X-RAY DIFFRACTIONr_scbond_other6.5398.491561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.06812.5612311
X-RAY DIFFRACTIONr_long_range_B_refined10.94993.1033690
X-RAY DIFFRACTIONr_long_range_B_other10.94893.1153691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.624→2.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 78 -
Rwork0.373 1521 -
obs--99.75 %

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