+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+96 | ||||||
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Title | Crystal structure of aminoglycoside 6'-acetyltransferase type Ii | ||||||
Components | Aminoglycoside 6'-acetyltransferase | ||||||
Keywords | TRANSFERASE / GNAT / acetyltransferase / aminoglycoside resistance | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Berghuis, A.M. / Burk, D.L. / Baettig, O.M. / Shi, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Febs J. / Year: 2016 Title: Comprehensive characterization of ligand-induced plasticity changes in a dimeric enzyme. Authors: Baettig, O.M. / Shi, K. / Yachnin, B.J. / Burk, D.L. / 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 | 5e96.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e96.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e96_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 5e96_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 5e96_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 5e96_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/5e96 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/5e96 | HTTPS FTP |
-Related structure data
Related structure data | 1n71S 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
#1: Protein | Mass: 20514.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: C238 / Gene: aac(6 )-II / Plasmid: pPLaac-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A099R279, UniProt: Q47764*PLUS |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40% ethylene glycol, 0.1 M phosphate-citrate pH 4.2, 0.1 M ammonium sulfate PH range: 4.2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 15426 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.206 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N71 Resolution: 2.1→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 53.98 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.12 Å / Total num. of bins used: 29 /
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Xplor file |
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