+Open data
-Basic information
Entry | Database: PDB / ID: 6m82 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TylM1 Y14paF bound to SAH and dTDP-phenol | ||||||
Components | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | ||||||
Keywords | TRANSFERASE / TylM1 / N-methyltransferase | ||||||
Function / homology | Function and homology information dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / antibiotic biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Streptomyces fradiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3971 Å | ||||||
Authors | Fick, R.J. / McDole, B.G. / Trievel, R.C. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Authors: Fick, R.J. / Horowitz, S. / McDole, B.G. / Clay, M.C. / Mehl, R.A. / Al-Hashimi, H.M. / Scheiner, S. / Trievel, R.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m82.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m82.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6m82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/6m82 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/6m82 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28536.896 Da / Num. of mol.: 1 / Mutation: Y14paF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylM1, tylMI / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI with pDULE2 paF plasmid References: UniProt: P95748, dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase |
---|---|
#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-TLO / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % / Mosaicity: 0.464 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: Precipitant: 23% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.3 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, ...Details: Precipitant: 23% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.3 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, 5 mM dTDP-phenol, 12 mg/mL TylM1 Y14paF Protein:Precipitant 4:2uL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3971→50 Å / Num. obs: 53915 / % possible obs: 98.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.58 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.01 / Rrim(I) all: 0.039 / Χ2: 1.052 / Net I/σ(I): 19.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3971→34.967 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.89
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.69 Å2 / Biso mean: 24.2216 Å2 / Biso min: 8.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3971→34.967 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
|