[English] 日本語
Yorodumi- PDB-5u18: Crystal structure of a methyltransferase involved in the biosynth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u18 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the Geneticin | ||||||
Components | N-3'' methyltransferase | ||||||
Keywords | TRANSFERASE / gentamicin methyltransferase SAH G418 | ||||||
Function / homology | Function and homology information S-adenosylmethionine-dependent methyltransferase activity / methylation / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Micromonospora echinospora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å | ||||||
Authors | Bury, P. / Huang, F. / Leadlay, P. / Dias, M.V.B. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5u18.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5u18.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 5u18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u18_validation.pdf.gz | 999.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5u18_full_validation.pdf.gz | 1002.8 KB | Display | |
Data in XML | 5u18_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5u18_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/5u18 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u18 | HTTPS FTP |
-Related structure data
Related structure data | 5tyqC 5u0nC 5u0tC 5u19C 5u1eC 5u1iC 5u4tC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35224.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: genN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2MG72 |
---|---|
#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-GET / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.54 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.195→48.854 Å / Num. obs: 16371 / % possible obs: 99.23 % / Redundancy: 2 % / Net I/σ(I): 13.64 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.195→48.854 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 80.14 Å2 / Biso mean: 31.4401 Å2 / Biso min: 13.02 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.195→48.854 Å
|