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- PDB-7q0q: Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q0q | |||||||||
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Title | Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B | |||||||||
![]() | Aminoglycoside N(3)-acetyltransferase III | |||||||||
![]() | ANTIBIOTIC / acetyltrasferase / aminoglycosides / inhibitor / complex | |||||||||
Function / homology | ![]() 2-deoxystreptamine metabolic process / antibiotic metabolic process / aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / acetyl-CoA catabolic process / coenzyme A binding / cellular response to antibiotic / protein homodimerization activity / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pontillo, N. / Guskov, A. | |||||||||
Funding support | European Union, 2items
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![]() | ![]() Title: The 3-N-alkylation of the neomycin B outmaneuvers the aminoglycoside resistant enzyme acetyltransferase(3)IIIa via an unexpected mechanism Authors: Pontillo, N. / Warszawik, E.M. / Partipilo, M. / Stetsenko, A. / Loznik, M. / Yang, X. / Slotboom, D.J. / Guskov, A. / Herrmann, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.9 KB | Display | ![]() |
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PDB format | ![]() | 98.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 906.2 KB | Display | ![]() |
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Full document | ![]() | 909.5 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q1xC ![]() 5ht0S ![]() 6mb9S ![]() 6np4S ![]() 7kesS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29429.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P29808, aminoglycoside 3-N-acetyltransferase |
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-Non-polymers , 6 types, 501 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/8I5.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/8I5.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-8I5 / | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Description: orthorombic |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 7-14% PEG 10,000, 0.1 M Na Acetate, 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→19.67 Å / Num. obs: 43209 / % possible obs: 99.13 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1743 / Net I/σ(I): 8.04 |
Reflection shell | Resolution: 1.96→2.03 Å / Num. unique obs: 3999 / CC1/2: 0.551 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ht0,7kes,6mb9,6np4 Resolution: 1.96→19.87 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.2587 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→19.87 Å
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Refine LS restraints |
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LS refinement shell |
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