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- PDB-7uy4: Aminoglycoside-modifying enzyme ANT-3,9 in complex with spectinom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uy4 | ||||||
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Title | Aminoglycoside-modifying enzyme ANT-3,9 in complex with spectinomycin and AMP-PNP | ||||||
![]() | Aminoglycoside (3'') (9) adenylyltransferase | ||||||
![]() | TRANSFERASE / Antibiotic resistance / Drug modifying enzymes / aminoglycoside / spectinonmycin / streptomycin / AMEs / ANTIMICROBIAL PROTEIN | ||||||
Function / homology | ![]() streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reeve, S.M. / Lee, R.E. / Das, N. / Jayaraman, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of the spectinomycin deactivating enzyme ANT-3,9 Authors: Das, N. / Reeve, S.M. / Lee, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.1 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xxqS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 256 / Label seq-ID: 1 - 256
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Components
#1: Protein | Mass: 28716.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: W8FS12, streptomycin 3''-adenylyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: 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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, pH 6.2 0.2M MgCl2 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 40924 / % possible obs: 98.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.97→2 Å / Rmerge(I) obs: 1.067 / Num. unique obs: 2573 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6xxq Resolution: 1.98→48.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.989 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.761 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→48.43 Å
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Refine LS restraints |
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