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Yorodumi- PDB-5f47: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f47 | |||||||||
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Title | Crystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with trehalose | |||||||||
Components | aminoglycoside acetyltransferase meta-AAC0020 | |||||||||
Keywords | TRANSFERASE / GNAT fold / GCN5-N-acetyltransferase fold / acetyltransferase / aminoglycoside / antibiotic resistance / metagenome / soil / coenzyme A / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information spermidine acetylation / spermidine binding / diamine N-acetyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | uncultured bacterium (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å | |||||||||
Authors | Xu, Z. / Skarina, T. / Wawrzak, Z. / Stogios, P.J. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: ACS Infect Dis / Year: 2017 Title: Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes. Authors: Xu, Z. / Stogios, P.J. / Quaile, A.T. / Forsberg, K.J. / Patel, S. / Skarina, T. / Houliston, S. / Arrowsmith, C. / Dantas, G. / Savchenko, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f47.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f47.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f47_validation.pdf.gz | 819.1 KB | Display | wwPDB validaton report |
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Full document | 5f47_full_validation.pdf.gz | 820.6 KB | Display | |
Data in XML | 5f47_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 5f47_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f47 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f47 | HTTPS FTP |
-Related structure data
Related structure data | 5f46C 5f48C 5f49C 5u08C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18526.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A059WZ16 #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350, 0.2 M calcium chloride, 10 mM neomycin, 2% trehalose, paratone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.497→30 Å / Num. obs: 51615 / % possible obs: 96.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.39 |
Reflection shell | Resolution: 1.497→1.53 Å / Redundancy: 4 % / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apoenzyme Resolution: 1.497→26.977 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.497→26.977 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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