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Yorodumi- PDB-4e8o: Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e8o | ||||||
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Title | Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-Ih from Acinetobacter baumannii | ||||||
Components | Aac(6')-Ih protein | ||||||
Keywords | TRANSFERASE / antibiotic resistance / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / GNAT superfamily / GCN5-related N-acetyltransferase superfamily / N-acetyltransferase fold / aminoglycoside antibiotic 6'-N-acetyltransferase / aminoglycoside antibiotics / acetyl coenzyme A / coenzyme A / intracellular | ||||||
Function / homology | Function and homology information aminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.138 Å | ||||||
Authors | Stogios, P.J. / Minasov, G. / Dong, A. / Evdokimova, E. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: ACS Infect Dis. / Year: 2017 Title: Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes. Authors: Stogios, P.J. / Kuhn, M.L. / Evdokimova, E. / Law, M. / Courvalin, P. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e8o.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8o.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8o ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8o | HTTPS FTP |
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-Related structure data
Related structure data | 4evyC 4f0yC 1s3zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19156.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: BM2686 / Gene: aac(6')-Ih / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q43899, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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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: 1.96 Å3/Da / Density % sol: 37.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 7, 2011 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.138→25 Å / Num. all: 16092 / Num. obs: 15384 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.033 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 2.138→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.05 / Rsym value: 0.151 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S3Z Resolution: 2.138→23.497 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 20.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.363 Å2 / ksol: 0.398 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.138→23.497 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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