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- PDB-5tuk: Crystal structure of tetracycline destructase Tet(51) -

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Basic information

Entry
Database: PDB / ID: 5tuk
TitleCrystal structure of tetracycline destructase Tet(51)
ComponentsTetracycline destructase Tet(51)
KeywordsOXIDOREDUCTASE / FAD-binding / tetracycline-inactivating / oxidoreductase activity
Function / homologyFAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Tetracycline destructase Tet(51)
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

Deposited unit
A: Tetracycline destructase Tet(51)
B: Tetracycline destructase Tet(51)
C: Tetracycline destructase Tet(51)
D: Tetracycline destructase Tet(51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,92812
Polymers185,4184
Non-polymers3,5118
Water16,970942
1
A: Tetracycline destructase Tet(51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2323
Polymers46,3541
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetracycline destructase Tet(51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2323
Polymers46,3541
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tetracycline destructase Tet(51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2323
Polymers46,3541
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tetracycline destructase Tet(51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2323
Polymers46,3541
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.490, 81.690, 127.130
Angle α, β, γ (deg.)90.00, 96.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tetracycline destructase Tet(51)


Mass: 46354.477 Da / Num. of mol.: 4
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)
Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H4TFU4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 942 / 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: 47.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.0, 10% PEG6000 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000028 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 21, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000028 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 144467 / % possible obs: 99.7 % / Redundancy: 3.77 % / CC1/2: 0.998 / Net I/σ(I): 11.93
Reflection shellHighest resolution: 1.85 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: 1.85→19.904 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.95
RfactorNum. reflection% reflection
Rfree0.1999 1997 1.38 %
Rwork0.1667 --
obs0.1672 144460 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11791 0 236 942 12969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712278
X-RAY DIFFRACTIONf_angle_d1.22416585
X-RAY DIFFRACTIONf_dihedral_angle_d15.5054551
X-RAY DIFFRACTIONf_chiral_restr0.0511777
X-RAY DIFFRACTIONf_plane_restr0.0082134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89620.28581400.25210113X-RAY DIFFRACTION99
1.8962-1.94750.261420.230310131X-RAY DIFFRACTION100
1.9475-2.00470.27571410.21510077X-RAY DIFFRACTION100
2.0047-2.06940.22981430.20310161X-RAY DIFFRACTION100
2.0694-2.14320.23661420.189710151X-RAY DIFFRACTION100
2.1432-2.22890.23161420.170910130X-RAY DIFFRACTION100
2.2289-2.33020.19021430.164310178X-RAY DIFFRACTION100
2.3302-2.45290.19121420.161110134X-RAY DIFFRACTION100
2.4529-2.60620.21951430.162110177X-RAY DIFFRACTION100
2.6062-2.8070.20371430.159510168X-RAY DIFFRACTION100
2.807-3.08850.21551430.1710225X-RAY DIFFRACTION100
3.0885-3.53330.19471430.160510188X-RAY DIFFRACTION100
3.5333-4.44340.15351440.138210248X-RAY DIFFRACTION100
4.4434-19.9050.1791460.155110382X-RAY DIFFRACTION100

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