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

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Basic information

Entry
Database: PDB / ID: 9hjv
TitleCrystal structure of flavin-dependent monooxygenase Tet(X4) in complex with prochlorperazine
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-P77 / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBeech, M.J. / Smith, H.G. / 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

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1196
Polymers41,6691
Non-polymers1,4505
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-42 kcal/mol
Surface area17100 Å2
Unit cell
Length a, b, c (Å)97.593, 97.593, 168.285
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

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


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-P77 / 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine


Mass: 373.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24ClN3S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 29 %w/v PEG4000, 0.1 M sodium citrate (pH 6.5), 0.1 M magnesium acetate, 0.1 M ammonium 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: 2.2→84.52 Å / Num. obs: 24742 / % possible obs: 99.8 % / Redundancy: 22 % / CC1/2: 0.991 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 2107 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→75.53 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 1270 5.14 %
Rwork0.1711 23422 -
obs0.1737 24692 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→75.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 93 279 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073167
X-RAY DIFFRACTIONf_angle_d0.88064304
X-RAY DIFFRACTIONf_chiral_restr0.0544456
X-RAY DIFFRACTIONf_plane_restr0.0064561
X-RAY DIFFRACTIONf_dihedral_angle_d17.77971233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.28991320.21132539X-RAY DIFFRACTION99.33
2.29-2.390.28551370.20392524X-RAY DIFFRACTION99
2.39-2.520.25261300.18842550X-RAY DIFFRACTION99.59
2.52-2.680.22381470.18062556X-RAY DIFFRACTION99.78
2.68-2.880.21381390.18562573X-RAY DIFFRACTION99.78
2.88-3.170.26291480.18352581X-RAY DIFFRACTION99.93
3.17-3.630.2481310.16142631X-RAY DIFFRACTION99.96
3.63-4.580.1531460.14152637X-RAY DIFFRACTION99.5
4.58-75.530.21851600.16712831X-RAY DIFFRACTION99.9
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)
11.8926435896-0.676481386621.013631346540.981665793838-0.445913899021.237996593150.00166289865881-0.025184986333-0.2106454049550.05446983501810.03456048537240.03447298776860.057503094928-0.0242180711323-0.03375480753460.1525905580360.007306935361330.03692253877570.153525620105-0.008571967284240.1597423454152.1682146382-34.6655682625-3.99009994252
22.07964078973-1.723624075381.10799950551.93876051176-0.8419349099030.937676642168-0.240915810433-0.1596474607380.16976784310.3407699377320.0830184856338-0.234603685876-0.192923911848-0.004129253392630.1502593392820.2618101447770.0073015449775-0.01932468987530.218248193063-0.003784424855540.1969140339928.47080698047-26.2862199732.6669865248
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 232 )12 - 2321 - 221
22chain 'A' and (resid 233 through 382 )233 - 382222 - 371

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