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Yorodumi- PDB-6vou: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vou | ||||||
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Title | Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-plazomicin and CoA | ||||||
Components | Aminoglycoside 2'-N-acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetyltransferase / GNAT superfamily | ||||||
Function / homology | Function and homology information gentamicin 2'-N-acetyltransferase / aminoglycoside 2'-N-acetyltransferase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | Providencia stuartii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Bassenden, A.V. / Berghuis, A.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Structural basis for plazomicin antibiotic action and resistance. Authors: Golkar, T. / Bassenden, A.V. / Maiti, K. / Arya, D.P. / Schmeing, T.M. / Berghuis, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vou.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vou.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/6vou ftp://data.pdbj.org/pub/pdb/validation_reports/vo/6vou | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20246.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Providencia stuartii (bacteria) / Gene: aac / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q52424, gentamicin 2'-N-acetyltransferase |
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-Non-polymers , 5 types, 124 molecules
#2: Chemical | #3: Chemical | ChemComp-TCE / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: acetyl CoA, plazomicin, LiCl, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63.66 Å / Num. obs: 33925 / % possible obs: 98.76 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05153 / Rpim(I) all: 0.0185 / Rrim(I) all: 0.05489 / Net I/σ(I): 18.89 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 3293 / CC1/2: 0.718 / CC star: 0.914 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→63.66 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0171 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: 46.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→63.66 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: -33.7750626502 Å / Origin y: 3.47799312622 Å / Origin z: -5.41677215527 Å
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Refinement TLS group | Selection details: all |