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- PDB-8er1: X-ray crystal structure of Tet(X6) -

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Basic information

Entry
Database: PDB / ID: 8er1
TitleX-ray crystal structure of Tet(X6)
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / Tetracycline destructase / FAD-linked reductases / FLAVOPROTEIN
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 / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesChryseobacterium oncorhynchi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4332
Polymers45,6481
Non-polymers7861
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.767, 52.485, 95.165
Angle α, β, γ (deg.)90.000, 95.880, 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.: 1
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 152 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium thiocyanate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.9 Å / Num. obs: 33653 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.1
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2240 / CC1/2: 0.976 / % possible all: 98

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Processing

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

6wg9


Resolution: 1.9→19.9 Å / SU ML: 0.2121 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.6626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 1999 5.96 %
Rwork0.1977 31548 -
obs0.2 33547 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 53 152 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123066
X-RAY DIFFRACTIONf_angle_d1.08634155
X-RAY DIFFRACTIONf_chiral_restr0.062458
X-RAY DIFFRACTIONf_plane_restr0.009537
X-RAY DIFFRACTIONf_dihedral_angle_d13.46321131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.32871390.27162189X-RAY DIFFRACTION96.72
1.95-20.28261440.24392246X-RAY DIFFRACTION98.35
2-2.060.28621400.242194X-RAY DIFFRACTION97.66
2.06-2.120.28551400.23422212X-RAY DIFFRACTION96.99
2.12-2.20.2521430.22932267X-RAY DIFFRACTION99.38
2.2-2.290.26481430.2172257X-RAY DIFFRACTION99.09
2.29-2.390.27241410.21922235X-RAY DIFFRACTION99.12
2.39-2.520.30161460.21262292X-RAY DIFFRACTION99.47
2.52-2.680.23921400.21782226X-RAY DIFFRACTION98.71
2.68-2.880.23331420.21872254X-RAY DIFFRACTION97.96
2.88-3.170.26681440.21722254X-RAY DIFFRACTION97.68
3.17-3.630.22911450.19322301X-RAY DIFFRACTION99.88
3.63-4.560.20151460.16492312X-RAY DIFFRACTION99.76

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