+Open data
-Basic information
Entry | Database: PDB / ID: 6np5 | ||||||
---|---|---|---|---|---|---|---|
Title | AAC-VIa bound to Kanamycin B | ||||||
Components | Aminoglycoside N(3)-acetyltransferase | ||||||
Keywords | TRANSFERASE / Antibiotic modifying enzyme / substrate selectivity / ANTIBIOTIC | ||||||
Function / homology | aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / metal ion binding / Chem-9CS / Aminoglycoside N(3)-acetyltransferase Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.353 Å | ||||||
Authors | Kumar, P. / Cuneo, M.J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Authors: Kumar, P. / Agarwal, P.K. / Waddell, M.B. / Mittag, T. / Serpersu, E.H. / Cuneo, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6np5.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6np5.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 6np5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/6np5 ftp://data.pdbj.org/pub/pdb/validation_reports/np/6np5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6np1C 6np2C 6np3C 6np4C 6ntiC 6ntjC 6o5uC 6bc6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28734.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: aac 3-VI / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q47030, aminoglycoside 3-N-acetyltransferase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-9CS / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | The T132S discrepancy arises from a SNP in the Enterobacteriaceae species | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % |
---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop Details: 15-20% polyethylene glycol (PEG) 8000,0.1 M Tris, pH=8.5 and 0.3 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 13, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→50 Å / Num. obs: 70419 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.45 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Rrim(I) all: 0.067 / Χ2: 0.663 / Net I/σ(I): 14.4 / Num. measured all: 225392 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BC6 Resolution: 1.353→43.214 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 13.43 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.62 Å2 / Biso mean: 27.4613 Å2 / Biso min: 12.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.353→43.214 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|