+Open data
-Basic information
Entry | Database: PDB / ID: 5yep | ||||||
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Title | Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis | ||||||
Components |
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Keywords | ANTITOXIN/TOXIN / toxin-antitoxin / HEPN-MNT / ANTITOXIN-TOXIN complex | ||||||
Function / homology | Function and homology information protein adenylyltransferase / toxin-antitoxin complex / RNA nuclease activity / nucleotidyltransferase activity / endonuclease activity / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Jia, X. / Gao, Z.Q. / Zhang, H. / Dong, Y.H. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system. Authors: Jia, X. / Yao, J. / Gao, Z. / Liu, G. / Dong, Y.H. / Wang, X. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yep.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yep.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/5yep ftp://data.pdbj.org/pub/pdb/validation_reports/ye/5yep | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15723.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_3165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH7 |
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#2: Protein | Mass: 16253.215 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_3166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ECH6 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Bicine (pH 8.6), 14% PEG6000 and 8% Ethlene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 14273 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.93 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.51 / Num. unique obs: 1904 / CC1/2: 0.949 / Rrim(I) all: 0.694 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→48.15 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.15 Å
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Refine LS restraints |
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LS refinement shell |
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