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- PDB-1j7l: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j7l | ||||||
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Title | Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa ADP Complex | ||||||
![]() | AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE | ||||||
![]() | TRANSFERASE / antibiotic resistance / kinase / ATP-binding | ||||||
Function / homology | ![]() kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burk, D.L. / Hon, W.C. / Leung, A.K.-W. / Berghuis, A.M. | ||||||
![]() | ![]() Title: Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase. Authors: Burk, D.L. / Hon, W.C. / Leung, A.K. / Berghuis, A.M. #1: ![]() Title: Structure of an Enzyme Required for Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases Authors: Hon, W.C. / McKay, G.A. / Thompson, P.R. / Sweet, R.M. / Yang, D.S.C. / Wright, G.D. / Berghuis, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.5 KB | Display | ![]() |
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PDB format | ![]() | 102.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 502.1 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 31012.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, magnesium acetate, sodium cacodylate, adenosine-5'-triphosphate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: Hon, W.C., (1997) Cell (Cambridge,Mass.), 89, 887. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.47 Å / Num. all: 95428 / Num. obs: 95428 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.2→2.34 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4389 / % possible all: 95.9 |
Reflection | *PLUS Num. obs: 30902 / Num. measured all: 95428 |
Reflection shell | *PLUS Lowest resolution: 2.28 Å / % possible obs: 95.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.45 Å2 / ksol: 0.3807 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.311 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.241 |