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- PDB-8twf: Crystal structure of tetracycline destructase Tet(56-3) -

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Basic information

Entry
Database: PDB / ID: 8twf
TitleCrystal structure of tetracycline destructase Tet(56-3)
Components6-hydroxynicotinate 3-monooxygenase
KeywordsOXIDOREDUCTASE / Inhibitor
Function / homology: / FAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / 6-hydroxynicotinate 3-monooxygenase
Function and homology information
Biological speciesLegionella massiliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKumar, H. / Tang, W.K. / Tolia, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2024
Title: Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes.
Authors: Blake, K.S. / Kumar, H. / Loganathan, A. / Williford, E.E. / Diorio-Toth, L. / Xue, Y.P. / Tang, W.K. / Campbell, T.P. / Chong, D.D. / Angtuaco, S. / Wencewicz, T.A. / Tolia, N.H. / Dantas, G.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 6-hydroxynicotinate 3-monooxygenase
A: 6-hydroxynicotinate 3-monooxygenase
B: 6-hydroxynicotinate 3-monooxygenase
C: 6-hydroxynicotinate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,9898
Polymers182,8474
Non-polymers3,1424
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.964, 134.282, 165.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
6-hydroxynicotinate 3-monooxygenase


Mass: 45711.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella massiliensis (bacteria) / Gene: BN59_03621 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A078L5T0
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.0 and 5%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.39→19.74 Å / Num. obs: 68420 / % possible obs: 99.6 % / Redundancy: 6.57 % / Biso Wilson estimate: 39.28 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.07
Reflection shellResolution: 2.39→2.52 Å / Num. unique obs: 6727 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.74 Å / SU ML: 0.293 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1288
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 1999 2.92 %
Rwork0.2189 66420 -
obs0.2197 68419 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12051 0 212 159 12422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003112523
X-RAY DIFFRACTIONf_angle_d0.526716963
X-RAY DIFFRACTIONf_chiral_restr0.04241846
X-RAY DIFFRACTIONf_plane_restr0.00482177
X-RAY DIFFRACTIONf_dihedral_angle_d13.37554523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31521390.26214608X-RAY DIFFRACTION98.24
2.46-2.520.28721410.24364698X-RAY DIFFRACTION99.98
2.52-2.60.29571410.23834703X-RAY DIFFRACTION99.98
2.6-2.680.27121420.24154712X-RAY DIFFRACTION99.98
2.68-2.780.28841410.23364691X-RAY DIFFRACTION100
2.78-2.890.27341420.23354709X-RAY DIFFRACTION99.98
2.89-3.020.30371410.23454712X-RAY DIFFRACTION99.96
3.02-3.180.29831430.2324731X-RAY DIFFRACTION99.98
3.18-3.380.24121430.22534759X-RAY DIFFRACTION99.96
3.38-3.630.25261430.22234721X-RAY DIFFRACTION99.98
3.64-40.23161430.20574768X-RAY DIFFRACTION99.98
4-4.570.191440.18964812X-RAY DIFFRACTION100
4.57-5.730.22721460.20154819X-RAY DIFFRACTION99.94
5.73-19.740.24271500.22564977X-RAY DIFFRACTION99.05

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