+Open data
-Basic information
Entry | Database: PDB / ID: 6sd6 | ||||||
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Title | Structure of VapBC from Shigella sonnei | ||||||
Components |
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Keywords | TOXIN / VapBC Toxin-antitoxin complex | ||||||
Function / homology | Function and homology information RNA nuclease activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | Shigella sonnei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Lea, S.M. / Hollingshead, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Polymorphisms in the VapBC toxin:antitoxin system mediate high frequency plasmid loss in Shigella sonnei Authors: Martyn, J.E. / Pilla, G. / Hollingshead, S. / Lea, S.M. / McVicker, G. / Tang, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sd6.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sd6.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sd6_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 6sd6_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 6sd6_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6sd6_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/6sd6 ftp://data.pdbj.org/pub/pdb/validation_reports/sd/6sd6 | HTTPS FTP |
-Related structure data
Related structure data | 3tndS 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: 8545.569 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella sonnei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3U1ZEK5 #2: Protein | Mass: 17035.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella sonnei (bacteria) / Gene: vapC, BZ172_30265 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0H9P9N5, Hydrolases; Acting on ester bonds #3: Water | ChemComp-HOH / | |
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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: 3.41 Å3/Da / Density % sol: 63.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium sulphate 0.3 M sodium formate 0.1 M sodium cacodylate pH 6.5 3% w/v PGA and 5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→83 Å / Num. obs: 19316 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.043 / Rrim(I) all: 0.134 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.61→2.65 Å / Rmerge(I) obs: 2.665 / Mean I/σ(I) obs: 1 / Num. unique obs: 922 / CC1/2: 0.502 / Rpim(I) all: 0.919 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TND Resolution: 2.61→35.15 Å / SU ML: 0.4114 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4172 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 80.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→35.15 Å
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Refine LS restraints |
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LS refinement shell |
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