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- PDB-5u4t: 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: 5u4t | ||||||
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Title | Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin | ||||||
![]() | Putative gentamicin methyltransferase | ||||||
![]() | TRANSFERASE / Methyltransferase | ||||||
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. | ||||||
![]() | ![]() 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 | ![]() | 129.5 KB | Display | ![]() |
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PDB format | ![]() | 101.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.6 KB | Display | ![]() |
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Full document | ![]() | 736.3 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tyqC ![]() 5u0nC ![]() 5u0tC ![]() 5u18C ![]() 5u19C ![]() 5u1eC ![]() 5u1iC 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: 35093.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Magnesium chloride, tris pH 8, peg 3350 and peg 400 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.086→48.028 Å / Num. obs: 17433 / % possible obs: 92.32 % / Redundancy: 2 % / Net I/σ(I): 24.15 |
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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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 93.13 Å2 / Biso mean: 28.2743 Å2 / Biso min: 7.09 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.086→48.028 Å
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