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Open data
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Basic information
Entry | Database: PDB / ID: 6p01 | |||||||||
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Title | Apo structure of the E52D mutant of ANT-4 | |||||||||
![]() | Kanamycin nucleotidyltransferase | |||||||||
![]() | TRANSFERASE/ANTIBIOTIC / Aminoglycoside nucelotidyl transferase (ANT) / Aminoglycoside modifying enzymes (AGMEs) / DNA polymerase / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex | |||||||||
Function / homology | ![]() nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Selvaraj, B. / Cuneo, M.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: "Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction Authors: Selvaraj, B. / Kocaman, S. / Trifas, M. / 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 | ![]() | 126.1 KB | Display | ![]() |
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PDB format | ![]() | 95.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p04C ![]() 6p06C ![]() 6p08C ![]() 1knyS 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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Components
#1: Protein | Mass: 29121.855 Da / Num. of mol.: 2 / Mutation: E52D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() References: UniProt: P05058, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 16-18% PEG 8K, 0.1 M Tris pH 7.5-8.0, 0.1-0.2 M MgCl2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→49.19 Å / Num. obs: 45256 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.054 / Rrim(I) all: 0.135 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3 / Num. unique obs: 2873 / CC1/2: 0.793 / Rpim(I) all: 0.281 / Rrim(I) all: 0.695 / Χ2: 0.69 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KNY Resolution: 1.89→49.185 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→49.185 Å
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Refine LS restraints |
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LS refinement shell |
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