+Open data
-Basic information
Entry | Database: PDB / ID: 4qc6 | ||||||
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Title | Crystal structure of aminoglycoside 6'-acetyltransferase-Ie | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | transferase/antibiotic / antibiotic resistance / GNAT family / acetyltransferase / acetylcoenzyme-A / aminoglycoside / transferase / transferase-antibiotic complex | ||||||
Function / homology | Function and homology information aminoglycoside 2''-phosphotransferase / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / kinase activity / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus warneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Smith, C.A. / Toth, M. / Weiss, T.M. / Frase, H. / Vakulenko, S.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis. Authors: Smith, C.A. / Toth, M. / Weiss, T.M. / Frase, H. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qc6.cif.gz | 195.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qc6.ent.gz | 156.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qc6_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4qc6_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4qc6_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4qc6_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/4qc6 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/4qc6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21735.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus warneri (bacteria) / Gene: aacA-aphD / Production host: Escherichia coli (E. coli) References: UniProt: Q7ATH7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: 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: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop Details: unbuffered 0.2 M ammonium formate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→19.941 Å / Num. all: 112448 / Num. obs: 112448 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.4 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→19.941 Å / SU ML: 0.09 / σ(F): 1.37 / Phase error: 14.85 / 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: 1.3→19.941 Å
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Refine LS restraints |
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LS refinement shell |
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