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- PDB-5tum: Crystal structure of tetracycline destructase Tet(56) -

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Basic information

Entry
Database: PDB / ID: 5tum
TitleCrystal structure of tetracycline destructase Tet(56)
Componentstetracycline destructase Tet(56)
KeywordsOXIDOREDUCTASE / FAD-binding / tetracycline-inactivating / oxidoreductase activity
Function / homologyOxidoreductases; 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 domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / response to antibiotic / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent monooxygenase
Function and homology information
Biological speciesLegionella longbeachae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.299 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(56)
B: tetracycline destructase Tet(56)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3204
Polymers92,7492
Non-polymers1,5712
Water0
1
A: tetracycline destructase Tet(56)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1602
Polymers46,3751
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tetracycline destructase Tet(56)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1602
Polymers46,3751
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.450, 114.010, 94.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein tetracycline destructase Tet(56)


Mass: 46374.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella longbeachae (bacteria) / Gene: LLO_2673 / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3HKY4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 2.23 Å3/Da / Density meas: 44.87 Mg/m3 / Density % sol: 44.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M trisodium citrate, pH 5.6, 10% PEG1000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000032 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 21, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000032 Å / Relative weight: 1
ReflectionResolution: 3.229→20 Å / Num. obs: 12805 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.996 / Net I/σ(I): 10.76
Reflection shellHighest resolution: 3.229 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.299→19.845 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.33
RfactorNum. reflection% reflection
Rfree0.2955 1285 10.04 %
Rwork0.2396 --
obs0.245 12803 99.01 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 3.299→19.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5819 0 106 0 5925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026041
X-RAY DIFFRACTIONf_angle_d0.6458172
X-RAY DIFFRACTIONf_dihedral_angle_d12.6612228
X-RAY DIFFRACTIONf_chiral_restr0.024888
X-RAY DIFFRACTIONf_plane_restr0.0021049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2991-3.43050.46061340.35521183X-RAY DIFFRACTION95
3.4305-3.58580.31021410.31761256X-RAY DIFFRACTION98
3.5858-3.77360.31151390.27641259X-RAY DIFFRACTION100
3.7736-4.00820.32471430.26381269X-RAY DIFFRACTION100
4.0082-4.31480.32681410.24771276X-RAY DIFFRACTION100
4.3148-4.74360.30921440.23031294X-RAY DIFFRACTION100
4.7436-5.41780.25111430.21251285X-RAY DIFFRACTION100
5.4178-6.78030.32411470.25251324X-RAY DIFFRACTION100
6.7803-19.84560.24091530.19091372X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 71.0382 Å / Origin y: 147.4638 Å / Origin z: 118.6993 Å
111213212223313233
T0.7887 Å20.02 Å20.1658 Å2-0.732 Å2-0.007 Å2--0.5426 Å2
L2.0659 °2-0.0543 °20.8994 °2-1.5882 °2-0.2402 °2--1.3235 °2
S-0.0125 Å °-0.3154 Å °-0.4218 Å °-0.1368 Å °-0.0258 Å °0.1024 Å °0.5017 Å °-0.2385 Å °0.0303 Å °
Refinement TLS groupSelection details: all

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