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

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Basic information

Entry
Database: PDB / ID: 9hjw
TitleCrystal structure of flavin-dependent monooxygenase Tet(X4) in complex with tegaserod
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 / 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 2, 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)42,8544
Polymers41,6691
Non-polymers1,1853
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-21 kcal/mol
Surface area16760 Å2
Unit cell
Length a, b, c (Å)97.286, 97.286, 167.673
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#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 electron density was not observed have not been 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
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-A1IVL / 1-[(~{E})-(5-methoxy-1~{H}-indol-3-yl)methylideneamino]-3-pentyl-guanidine


Mass: 301.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate 0.1 M Sodium citrate tribasic dihydrate pH 5.6 30 % Polyethylene glycol 4,000

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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: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→59.43 Å / Num. obs: 37807 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2389 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.43 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1900 5.04 %
Rwork0.1769 --
obs0.1786 37715 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→59.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 80 361 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073164
X-RAY DIFFRACTIONf_angle_d0.9454299
X-RAY DIFFRACTIONf_dihedral_angle_d12.281421
X-RAY DIFFRACTIONf_chiral_restr0.063457
X-RAY DIFFRACTIONf_plane_restr0.007565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.29261160.22732501X-RAY DIFFRACTION99
1.95-20.2521290.20472499X-RAY DIFFRACTION100
2-2.060.22341380.19112506X-RAY DIFFRACTION100
2.06-2.120.23621470.19272502X-RAY DIFFRACTION100
2.12-2.20.20891220.18392517X-RAY DIFFRACTION100
2.2-2.290.24521570.18792498X-RAY DIFFRACTION100
2.29-2.390.22111320.18872525X-RAY DIFFRACTION100
2.39-2.520.24921290.19512544X-RAY DIFFRACTION100
2.52-2.680.2511310.19882553X-RAY DIFFRACTION100
2.68-2.880.23261430.20842543X-RAY DIFFRACTION100
2.88-3.170.22041300.1942587X-RAY DIFFRACTION100
3.17-3.630.20921340.16842592X-RAY DIFFRACTION100
3.63-4.570.16761540.1372631X-RAY DIFFRACTION100
4.58-59.430.17691380.16992817X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5408-0.77220.83141.3066-0.40921.2177-0.0066-0.0149-0.17670.11920.01830.01880.053-0.0128-0.02250.1932-0.00140.0350.1949-0.0050.20272.3665-34.1838-4.1042
23.202-1.77880.71511.5910.0740.7851-0.02090.05050.26670.173-0.001-0.5125-0.0540.19350.03270.25910.0038-0.04890.26120.02480.287421.6096-33.33723.7331
32.2299-1.04830.81111.9894-0.33991.1202-0.1862-0.32430.04620.38820.1379-0.0418-0.0898-0.13310.07680.30610.0320.01650.2326-0.00510.1841-2.198-21.44032.1128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 226 )
2X-RAY DIFFRACTION2chain 'A' and (resid 227 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 382 )

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