+Open data
-Basic information
Entry | Database: PDB / ID: 3q8x | ||||||
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Title | Structure of a toxin-antitoxin system bound to its substrate | ||||||
Components |
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Keywords | TRANSFERASE / Polynucleotide kinase fold / epsilon: antidote zeta: bacterial toxin | ||||||
Function / homology | Function and homology information negative regulation of cell killing / UDP-N-acetylglucosamine kinase / toxic substance binding / response to toxic substance / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | Mutschler, H. / Gebhardt, M. / Shoeman, R.L. / Meinhart, A. | ||||||
Citation | Journal: Plos Biol. / Year: 2011 Title: A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. Authors: Mutschler, H. / Gebhardt, M. / Shoeman, R.L. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q8x.cif.gz | 298 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q8x.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/3q8x ftp://data.pdbj.org/pub/pdb/validation_reports/q8/3q8x | HTTPS FTP |
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-Related structure data
Related structure data | 1gvnS 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: 10734.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: epsilon / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6UZC8, UniProt: Q57231*PLUS #2: Protein | Mass: 32444.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54944 #3: Chemical | #4: Chemical | ChemComp-UD1 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.2 M sodium acetate, 16% (w/v) PEG1500 and 7% (v/v) MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2010 |
Radiation | Monochromator: fixed-exit Si(111) monomchromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 26528 / Num. obs: 25432 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.1 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GVN Resolution: 2.7→46.52 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 31.514 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.016 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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