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- PDB-21cf: Crystal structure of sulX in complex with FMN and sulfadimethoxine -

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Basic information

Entry
Database: PDB / ID: 21cf
TitleCrystal structure of sulX in complex with FMN and sulfadimethoxine
ComponentsSulfonamide monooxygenase
KeywordsOXIDOREDUCTASE / FMN-dependent / Sulfonamide degradation / Sulfonamide resistance
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: 2.37 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
DepositionDec 7, 2025Deposition 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)47,2359
Polymers45,9641
Non-polymers1,2718
Water1,67593
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)188,94236
Polymers183,8574
Non-polymers5,08532
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 area12370 Å2
ΔGint-73 kcal/mol
Surface area52250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.963, 133.963, 139.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21A-684-

HOH

31A-686-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfonamide monooxygenase


Mass: 45964.262 Da / Num. of mol.: 1
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, 101 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-A1E1Y / Sulfadimethoxine / 4-azanyl-~{N}-(2,6-dimethoxypyrimidin-4-yl)benzenesulfonamide


Mass: 310.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 24% PEG 500, 1.2 mM Zinc sulfate, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→25 Å / Num. obs: 30267 / % possible obs: 98.4 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 27.54
Reflection shellResolution: 2.37→2.45 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2917 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→24.87 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.696 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26647 1483 5.1 %RANDOM
Rwork0.20928 ---
obs0.2122 27324 93.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å2-0 Å2
3----4.6 Å2
Refinement stepCycle: 1 / Resolution: 2.37→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 74 93 3184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133149
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172841
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6674291
X-RAY DIFFRACTIONr_angle_other_deg1.3251.5876544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98121.329173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3915472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7431528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023599
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_it5.6336.831575
X-RAY DIFFRACTIONr_mcbond_other5.6326.831574
X-RAY DIFFRACTIONr_mcangle_it7.56510.2221967
X-RAY DIFFRACTIONr_mcangle_other7.56310.2221968
X-RAY DIFFRACTIONr_scbond_it6.2797.3061573
X-RAY DIFFRACTIONr_scbond_other6.1247.2911570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0710.7832319
X-RAY DIFFRACTIONr_long_range_B_refined9.70878.8853677
X-RAY DIFFRACTIONr_long_range_B_other9.70778.8953678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.37→2.422 Å
RfactorNum. reflection% reflection
Rfree0.388 114 -
Rwork0.366 1850 -
obs--88.51 %

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