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- PDB-21cv: Crystal structure of sulX in complex with FMN and sulfamethoxypyr... -

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Basic information

Entry
Database: PDB / ID: 21cv
TitleCrystal structure of sulX in complex with FMN and sulfamethoxypyridazine
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 / TRIETHYLENE GLYCOL / Sulfonamide monooxygenase
Similarity search - Component
Biological speciesMicrobacterium sp. CJ77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 8, 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)47,35610
Polymers45,9641
Non-polymers1,3919
Water4,053225
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)189,42240
Polymers183,8574
Non-polymers5,56536
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 area12210 Å2
ΔGint-74 kcal/mol
Surface area52540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.916, 133.916, 139.504
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-812-

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 , 7 types, 234 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-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-A1E1X / Sulfamethoxypyridazine / 4-azanyl-~{N}-(6-methoxypyridazin-3-yl)benzenesulfonamide


Mass: 280.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N4O3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 24%PEG 500, 1.2 mM Zinc sulfate, 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: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→25 Å / Num. obs: 43884 / % possible obs: 98.9 % / Redundancy: 11.3 % / CC1/2: 0.996 / Net I/σ(I): 22.13
Reflection shellResolution: 2.09→2.16 Å / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4351 / CC1/2: 0.93

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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: 2.09→24.91 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.394 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22645 2218 5.1 %RANDOM
Rwork0.18048 ---
obs0.18275 41583 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.696 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.82 Å20 Å2
2--1.65 Å2-0 Å2
3----5.35 Å2
Refinement stepCycle: 1 / Resolution: 2.09→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 82 225 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133168
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172865
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6664313
X-RAY DIFFRACTIONr_angle_other_deg1.4041.5856600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07821.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56715475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it4.8865.9881580
X-RAY DIFFRACTIONr_mcbond_other4.8865.9881579
X-RAY DIFFRACTIONr_mcangle_it5.9758.9531975
X-RAY DIFFRACTIONr_mcangle_other5.9748.9531976
X-RAY DIFFRACTIONr_scbond_it6.0786.4161587
X-RAY DIFFRACTIONr_scbond_other6.0766.4161588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9149.4622339
X-RAY DIFFRACTIONr_long_range_B_refined8.98571.2123867
X-RAY DIFFRACTIONr_long_range_B_other8.98471.2043868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.141 Å
RfactorNum. reflection% reflection
Rfree0.33 157 -
Rwork0.292 3023 -
obs--99.16 %

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