[English] 日本語
![](img/lk-miru.gif)
- PDB-6vou: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vou | ||||||
---|---|---|---|---|---|---|---|
Title | Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-plazomicin and CoA | ||||||
![]() | Aminoglycoside 2'-N-acetyltransferase | ||||||
![]() | TRANSFERASE / Acetyltransferase / GNAT superfamily | ||||||
Function / homology | ![]() gentamicin 2'-N-acetyltransferase / aminoglycoside 2'-N-acetyltransferase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bassenden, A.V. / Berghuis, A.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for plazomicin antibiotic action and resistance. Authors: Golkar, T. / Bassenden, A.V. / Maiti, K. / Arya, D.P. / Schmeing, T.M. / Berghuis, A.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 199 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20246.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q52424, gentamicin 2'-N-acetyltransferase |
---|
-Non-polymers , 5 types, 124 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/TCE.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PZC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TCE.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PZC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TCE / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: acetyl CoA, plazomicin, LiCl, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63.66 Å / Num. obs: 33925 / % possible obs: 98.76 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05153 / Rpim(I) all: 0.0185 / Rrim(I) all: 0.05489 / Net I/σ(I): 18.89 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 3293 / CC1/2: 0.718 / CC star: 0.914 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→63.66 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -33.7750626502 Å / Origin y: 3.47799312622 Å / Origin z: -5.41677215527 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |