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- PDB-4dbx: Crystal structure of aminoglycoside phosphotransferase APH(2")-ID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dbx | |||||||||
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Title | Crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA | |||||||||
![]() | APH(2")-ID | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stogios, P.J. / Minasov, G. / Tan, K. / Nocek, B. / Singer, A.U. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. ...Stogios, P.J. / Minasov, G. / Tan, K. / Nocek, B. / Singer, A.U. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. / Wright, G.D. / Savchenko, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | |||||||||
![]() | ![]() Title: A small molecule discrimination map of the antibiotic resistance kinome. Authors: Shakya, T. / Stogios, P.J. / Waglechner, N. / Evdokimova, E. / Ejim, L. / Blanchard, J.E. / McArthur, A.G. / Savchenko, A. / Wright, G.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.1 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4de4C ![]() 4dfbC ![]() 4dfuC 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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Unit cell |
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Components
#1: Protein | Mass: 38279.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 10% PEG 6K, 5% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 25489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.088 / Net I/σ(I): 34.04 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.13 / Rsym value: 0.508 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.226 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.004→30.269 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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