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Open data
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Basic information
Entry | Database: PDB / ID: 8er0 | |||||||||
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Title | X-ray crystal structure of Tet(X6) bound to anhydrotetracycline | |||||||||
![]() | Flavin-dependent monooxygenase | |||||||||
![]() | OXIDOREDUCTASE/INHIBITOR / Tetracycline destructase / FAD-linked reductases / ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kumar, H. / Tolia, N.H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 538.1 KB | Display | ![]() |
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PDB format | ![]() | 367.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8er1C ![]() 6wg9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45647.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tet(X) / Production host: ![]() ![]() ![]() 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, ![]() #2: Chemical | #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure![]() ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.9236748906 Å / Origin y: 4.75860543734 Å / Origin z: 24.5904379495 Å
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Refinement TLS group | Selection details: all |