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Yorodumi- PDB-7jzs: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jzs | ||||||
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Title | Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with 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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Park, J. / Bassenden, A.V. / Berghuis, A.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Sci Rep / Year: 2021 Title: Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2') enzymes. Authors: Bassenden, A.V. / Dumalo, L. / Park, J. / Blanchet, J. / Maiti, K. / Arya, D.P. / 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 | 7jzs.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzs.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jzs_validation.pdf.gz | 729.8 KB | Display | wwPDB validaton report |
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Full document | 7jzs_full_validation.pdf.gz | 737.2 KB | Display | |
Data in XML | 7jzs_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 7jzs_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzs ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzs | HTTPS FTP |
-Related structure data
Related structure data | 6vr2C 6vr3C 6vtaC 5us1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20634.213 Da / Num. of mol.: 1 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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#2: Chemical | ChemComp-COA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium sulfate, PEG 400, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→52.75 Å / Num. obs: 52444 / % possible obs: 99.95 % / Redundancy: 12.1 % / CC1/2: 1 / Net I/σ(I): 28.09 |
Reflection shell | Resolution: 1.3→1.346 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 5117 / CC1/2: 0.646 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5US1 Resolution: 1.3→52.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.521 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 27.641 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→52.75 Å
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Refine LS restraints |
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