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- PDB-5u1e: Crystal structure of a methyltransferase involved in the biosynth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u1e | ||||||
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Title | Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the kanamycin B | ||||||
![]() | Putative gentamicin methyltransferase | ||||||
![]() | TRANSFERASE / gentamicin methyltransferase SAH kanamycin B | ||||||
Function / homology | ![]() S-adenosylmethionine-dependent methyltransferase activity / methylation / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bury, P. / Huang, F. / Leadlay, P. / Dias, M.V.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis. Authors: Bury, P.D.S. / Huang, F. / Li, S. / Sun, Y. / Leadlay, P.F. / Dias, M.V.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tyqC ![]() 5u0nC ![]() 5u0tC ![]() 5u18C ![]() 5u19C ![]() 5u1iC ![]() 5u4tSC C: citing same article ( S: Starting model for refinement |
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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: 37395.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9CS / ( |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride, tris pH 8, peg 3350, peg 400 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 2.213→48.77 Å / Num. obs: 30510 / % possible obs: 99.73 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U4T Resolution: 2.213→48.768 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.16 Å2 / Biso mean: 36.9949 Å2 / Biso min: 17.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.213→48.768 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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