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Open data
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Basic information
Entry | Database: PDB / ID: 6jiv | ||||||
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Title | SspE crystal structure | ||||||
![]() | SspE protein | ||||||
![]() | HYDROLASE / DNase / PT | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bing, Y.Z. / Yang, H.G. | ||||||
![]() | ![]() Title: SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Authors: Xiong, X. / Wu, G. / Wei, Y. / Liu, L. / Zhang, Y. / Su, R. / Jiang, X. / Li, M. / Gao, H. / Tian, X. / Zhang, Y. / Hu, L. / Chen, S. / Tang, Y. / Jiang, S. / Huang, R. / Li, Z. / Wang, Y. / ...Authors: Xiong, X. / Wu, G. / Wei, Y. / Liu, L. / Zhang, Y. / Su, R. / Jiang, X. / Li, M. / Gao, H. / Tian, X. / Zhang, Y. / Hu, L. / Chen, S. / Tang, Y. / Jiang, S. / Huang, R. / Li, Z. / Wang, Y. / Deng, Z. / Wang, J. / Dedon, P.C. / Chen, S. / Wang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.9 KB | Display | ![]() |
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PDB format | ![]() | 324.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.1 KB | Display | ![]() |
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Full document | ![]() | 598.2 KB | Display | |
Data in XML | ![]() | 87 KB | Display | |
Data in CIF | ![]() | 115.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 87803.883 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.66 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG MME 5000, HEPES pH 7.0, Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 30, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.31→125.33 Å / Num. obs: 64318 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 8.58 |
Reflection shell | Resolution: 3.3→3.5 Å / Num. unique obs: 52096 / CC1/2: 0.998 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 346.76 Å2 / Biso mean: 99.711 Å2 / Biso min: 29.02 Å2
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Refinement step | Cycle: final / Resolution: 3.31→125.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.313→3.399 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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