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Open data
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Basic information
Entry | Database: PDB / ID: 6mb9 | ||||||
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Title | Ternary (neomycin/CoA) structure of AAC-IIIb | ||||||
![]() | Aac(3)-IIIb protein | ||||||
![]() | TRANSFERASE/ANTIBIOTIC / acetyltransferase / promiscuity / GNAT / antibiotic resistance / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex | ||||||
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 / COENZYME A / NEOMYCIN / Aminoglycoside N(3)-acetyltransferase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuneo, M.J. / Kumar, P. | ||||||
![]() | ![]() Title: Encoding of Promiscuity in an Aminoglycoside Acetyltransferase. Authors: Kumar, P. / Selvaraj, B. / Serpersu, E.H. / Cuneo, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.6 KB | Display | ![]() |
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PDB format | ![]() | 179.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 45.8 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mb4C ![]() 6mb5C ![]() 6mb6C ![]() 6mb7C ![]() 6mb8C ![]() 6bc3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 29018.799 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-2PE / | #4: Chemical | ChemComp-NMY / #5: Water | ChemComp-HOH / | Sequence details | see NCBI Reference Sequence: WP_088170001.1 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14-22% PEG 3350 and 0.1-0.4M sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 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: 2.5→50 Å / Num. obs: 37666 / % possible obs: 97.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.98 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.073 / Rrim(I) all: 0.108 / Χ2: 0.573 / Net I/σ(I): 4.9 / Num. measured all: 72266 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BC3 Resolution: 2.5→48.8 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.21 Å2 / Biso mean: 30.9665 Å2 / Biso min: 14.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.8 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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