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Yorodumi- PDB-5f46: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f46 | ||||||
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Title | Crystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample, apoenzyme form | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Xu, Z. / Skarina, T. / 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 | 5f46.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f46.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f46_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 5f46_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 5f46_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5f46_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f46 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f46 | HTTPS FTP |
-Related structure data
Related structure data | 5f47C 5f48C 5f49C 5u08C 4yfjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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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: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 33193 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 0.577 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.405 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YFJ Resolution: 1.85→29.842 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.08 / 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: 1.85→29.842 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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