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- PDB-9hke: Crystal structure of flavin-dependent monooxygenase Tet(X4) in co... -

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Basic information

Entry
Database: PDB / ID: 9hke
TitleCrystal structure of flavin-dependent monooxygenase Tet(X4) in complex with trifluoperazine
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / Flavin-dependent monooxygenase Tet(X4)
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / FAD binding / monooxygenase activity / response to antibiotic / cytoplasm
Similarity search - Function
Flavin-dependent monooxygenase TetX / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Chem-TFP / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmith, H.G. / Beech, M.J. / Allen, M.D. / Farley, A.J.M. / Schofield, C.J.
Funding support1items
OrganizationGrant numberCountry
Other privateIneos Oxford Institute Core Grant
CitationJournal: Chem Sci / Year: 2025
Title: Binding assays enable discovery of Tet(X) inhibitors that combat tetracycline destructase resistance.
Authors: Beech, M.J. / Toma, E.C. / Smith, H.G. / Trush, M.M. / Ang, J.H.J. / Wong, M.Y. / Wong, C.H.J. / Ali, H.S. / Butt, Z. / Goel, V. / Duarte, F. / Farley, A.J.M. / Walsh, T.R. / Schofield, C.J.
History
DepositionDec 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0525
Polymers41,6691
Non-polymers1,3834
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-8 kcal/mol
Surface area16800 Å2
Unit cell
Length a, b, c (Å)97.662, 97.662, 168.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent monooxygenase / TetX monooxygenase / TetX


Mass: 41668.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues for which there was little to no electron density (eg 246-248) were not modelled.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mtr-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 5 types, 413 molecules

#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE


Mass: 407.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24F3N3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 27 % PEG 3350 0.1 M Bis-Tris propane pH 7.0 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→48.82 Å / Num. obs: 38081 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 26.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2390 / CC1/2: 0.843 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.7 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 1911 5.03 %
Rwork0.1822 36085 -
obs0.1847 37996 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 92 409 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823198
X-RAY DIFFRACTIONf_angle_d0.99244358
X-RAY DIFFRACTIONf_chiral_restr0.06458
X-RAY DIFFRACTIONf_plane_restr0.0091566
X-RAY DIFFRACTIONf_dihedral_angle_d23.2507474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.29491130.27322523X-RAY DIFFRACTION99.58
1.95-20.35751360.23822535X-RAY DIFFRACTION99.96
2-2.060.27151400.21632503X-RAY DIFFRACTION99.96
2.06-2.130.26631410.20712535X-RAY DIFFRACTION99.93
2.13-2.20.23561290.19332527X-RAY DIFFRACTION99.92
2.2-2.290.25131490.20362522X-RAY DIFFRACTION100
2.29-2.390.29111370.19172552X-RAY DIFFRACTION100
2.39-2.520.23891320.19252557X-RAY DIFFRACTION100
2.52-2.680.23161330.1832564X-RAY DIFFRACTION100
2.68-2.880.22791400.18612576X-RAY DIFFRACTION100
2.88-3.170.2481350.19542589X-RAY DIFFRACTION99.96
3.18-3.630.21741350.17462620X-RAY DIFFRACTION100
3.63-4.580.17821540.1462639X-RAY DIFFRACTION100
4.58-46.70.22321370.16962843X-RAY DIFFRACTION99.83

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