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- PDB-5tuf: Crystal structure of tetracycline destructase Tet(50) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5tuf
TitleCrystal structure of tetracycline destructase Tet(50) in complex with anhydrotetracycline
ComponentsTetracycline destructase Tet(50)
KeywordsOXIDOREDUCTASE / FAD-binding / tetracycline-inactivating / oxidoreductase activity
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 / oxidoreductase activity / response to antibiotic
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5A,6-ANHYDROTETRACYCLINE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPark, J. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI123394-01 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes.
Authors: Park, J. / Gasparrini, A.J. / Reck, M.R. / Symister, C.T. / Elliott, J.L. / Vogel, J.P. / Wencewicz, T.A. / Dantas, G. / Tolia, N.H.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetracycline destructase Tet(50)
B: Tetracycline destructase Tet(50)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,63412
Polymers91,9642
Non-polymers2,67010
Water6,071337
1
A: Tetracycline destructase Tet(50)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1526
Polymers45,9821
Non-polymers1,1705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetracycline destructase Tet(50)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4826
Polymers45,9821
Non-polymers1,5005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.990, 107.370, 152.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tetracycline destructase Tet(50)


Mass: 45982.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Isolated from functional metagenomic selections from agricultural and grassland soils.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Details (production host): pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059WYP6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


Mass: 426.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.0-6.5, 1.6-2.0 M ammonium sulfate, 2-10% 1,4-dioxane
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000031 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 21, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 40157 / % possible obs: 98.6 % / Redundancy: 4.93 % / CC1/2: 0.997 / Net I/σ(I): 13.57
Reflection shellHighest resolution: 2.25 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.791 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 1402 3.52 %
Rwork0.2068 --
obs0.2084 39793 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→19.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5998 0 172 337 6507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036296
X-RAY DIFFRACTIONf_angle_d0.7428526
X-RAY DIFFRACTIONf_dihedral_angle_d14.4892307
X-RAY DIFFRACTIONf_chiral_restr0.031922
X-RAY DIFFRACTIONf_plane_restr0.0031080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33030.4711140.42373167X-RAY DIFFRACTION82
2.3303-2.42350.29851440.24923865X-RAY DIFFRACTION100
2.4235-2.53350.26541370.23493842X-RAY DIFFRACTION100
2.5335-2.66680.29661420.22273860X-RAY DIFFRACTION100
2.6668-2.83350.27481440.22533916X-RAY DIFFRACTION100
2.8335-3.05150.2761390.22273862X-RAY DIFFRACTION100
3.0515-3.35720.26961430.2063914X-RAY DIFFRACTION100
3.3572-3.840.28381440.19653892X-RAY DIFFRACTION99
3.84-4.82630.18981440.15553959X-RAY DIFFRACTION100
4.8263-19.79130.19391510.17634114X-RAY DIFFRACTION99

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