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Open data
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Basic information
Entry | Database: PDB / ID: 7lao | ||||||
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Title | Crystal structure of aminoglycoside acetyltransferase AAC(3)-IIb | ||||||
![]() | Aminoglycoside N(3)-acetyltransferase III | ||||||
![]() | TRANSFERASE / AAC(3)-IIb / RESISTANCE / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID | ||||||
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 / Aminoglycoside N(3)-acetyltransferase III![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stogios, P.J. / Evdokimova, E. / Osipiuk, J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family. Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, 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 | ![]() | 140.2 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ht0C ![]() 6mmzC ![]() 6mn0C ![]() 6mn3C ![]() 6mn4C ![]() 6mn5C ![]() 7kesC ![]() 7lapC ![]() 6bc3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 29017.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q01515, aminoglycoside 3-N-acetyltransferase |
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#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M citric acid, Bis-tris propane pH 6.4, 25% (w/v) PEG3350, 2 mM magnesium chloride, 1 mM tobramycin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→40 Å / Num. obs: 22563 / % possible obs: 95.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.92→1.95 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 935 / CC1/2: 0.983 / Rpim(I) all: 0.159 / % possible all: 79.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6bc3 Resolution: 1.92→35.32 Å / SU ML: 0.2062 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3955 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: 50.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→35.32 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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