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Yorodumi- PDB-5u0t: Crystal structure of a methyltransferase involved in the biosynth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u0t | ||||||
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Title | Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside | ||||||
Components | Putative gentamicin methyltransferase | ||||||
Keywords | TRANSFERASE / gentamicin methyltransferase | ||||||
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: 2.109 Å | ||||||
Authors | Bury, P. / Huang, F. / Leadlay, P. / Dias, M.V.B. | ||||||
Funding support | Brazil, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u0t.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u0t.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/5u0t ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u0t | HTTPS FTP |
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-Related structure data
Related structure data | 5tyqC 5u0nC 5u18C 5u19C 5u1eC 5u1iC 5u4tSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Micromonospora echinospora (bacteria) / Gene: genN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2MG72 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-7QM / ( |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: magnesium chloride, tris pH 8,0, peg 3350 and peg 400 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 16, 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: 2.109→43.58 Å / Num. obs: 17891 / % possible obs: 99.59 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.1074 / Net I/σ(I): 19.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U4T Resolution: 2.109→43.575 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.65 Å2 / Biso mean: 25.1031 Å2 / Biso min: 7.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.109→43.575 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: 6
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