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- PDB-8er0: X-ray crystal structure of Tet(X6) bound to anhydrotetracycline -

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Basic information

Entry
Database: PDB / ID: 8er0
TitleX-ray crystal structure of Tet(X6) bound to anhydrotetracycline
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / Tetracycline destructase / FAD-linked reductases / FLAVOPROTEIN / OXIDOREDUCTASE-INHIBITOR complex
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
FLAVIN-ADENINE DINUCLEOTIDE / 5A,6-ANHYDROTETRACYCLINE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesChryseobacterium oncorhynchi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKumar, H. / Tolia, N.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2U01AI123394 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Intramural Research Program United States
CitationJournal: Commun Biol / Year: 2023
Title: Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases.
Authors: Kumar, H. / Williford, E.E. / Blake, K.S. / Virgin-Downey, B. / Dantas, G. / Wencewicz, T.A. / Tolia, N.H.
History
DepositionOct 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase
B: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7196
Polymers91,2952
Non-polymers2,4244
Water4,738263
1
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8603
Polymers45,6481
Non-polymers1,2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8603
Polymers45,6481
Non-polymers1,2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.086, 52.212, 94.871
Angle α, β, γ (deg.)90.000, 95.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Flavin-dependent monooxygenase / TetX monooxygenase / TetX


Mass: 45647.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium oncorhynchi (bacteria)
Gene: tet(X) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A316WTJ0, 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: A0A316WTJ0, 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-TDC / 5A,6-ANHYDROTETRACYCLINE


Mass: 426.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N2O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Potassium thiocyanate

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→19.84 Å / Num. obs: 43044 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.64 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3705 / CC1/2: 0.71 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WG9

6wg9


Resolution: 2.2→19.84 Å / SU ML: 0.2225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2313 2003 4.66 %
Rwork0.1925 40939 -
obs0.1944 42942 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 168 263 6308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036172
X-RAY DIFFRACTIONf_angle_d0.59418382
X-RAY DIFFRACTIONf_chiral_restr0.0429918
X-RAY DIFFRACTIONf_plane_restr0.00531083
X-RAY DIFFRACTIONf_dihedral_angle_d13.83712294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.28981380.25442858X-RAY DIFFRACTION97.02
2.25-2.320.26461370.22732919X-RAY DIFFRACTION99.22
2.32-2.380.22961420.22272907X-RAY DIFFRACTION99.22
2.38-2.460.29561510.21982918X-RAY DIFFRACTION99.32
2.46-2.550.31631280.21552938X-RAY DIFFRACTION99.32
2.55-2.650.26821510.21552916X-RAY DIFFRACTION99.42
2.65-2.770.23031430.21492943X-RAY DIFFRACTION99.45
2.77-2.920.281400.20892941X-RAY DIFFRACTION99.29
2.92-3.10.25511490.21542866X-RAY DIFFRACTION96.91
3.1-3.340.26161370.19862805X-RAY DIFFRACTION95.64
3.34-3.670.21011460.17982984X-RAY DIFFRACTION99.75
3.67-4.20.18041470.16842964X-RAY DIFFRACTION99.94
4.2-5.270.18331450.14763006X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: -21.9236748906 Å / Origin y: 4.75860543734 Å / Origin z: 24.5904379495 Å
111213212223313233
T0.234300194767 Å2-0.00471880109014 Å20.000806795629943 Å2-0.169330240339 Å20.0087793420769 Å2--0.212097489712 Å2
L0.279986721021 °2-0.0269190801021 °2-0.03326412065 °2-0.158037402085 °20.0664034474783 °2--0.318229539391 °2
S0.00530246916117 Å °-0.0868569358822 Å °-0.00546654099523 Å °-0.00982386944929 Å °0.0106006141303 Å °0.0358180347045 Å °0.00808523144996 Å °0.000909821035745 Å °-0.0175681754086 Å °
Refinement TLS groupSelection details: all

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