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Yorodumi- PDB-8g0k: Bacteroides multispecies type VI secretion system Ntox15 domain e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g0k | ||||||
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Title | Bacteroides multispecies type VI secretion system Ntox15 domain effector and immunity Tde1/Tdi1 | ||||||
Components |
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Keywords | TOXIN / type VI secretion system / Bacteroides / effector / immunity | ||||||
Biological species | Bacteroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bosch, D.E. / Mougous, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mbio / Year: 2023 Title: Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales. Authors: Bosch, D.E. / Abbasian, R. / Parajuli, B. / Peterson, S.B. / Mougous, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g0k.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g0k.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 8g0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g0k_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 8g0k_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 8g0k_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8g0k_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0k ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22863.316 Da / Num. of mol.: 2 / Mutation: H279A, D282A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides (bacteria) / Production host: Escherichia coli BL21 (bacteria) #2: Protein | Mass: 22856.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides (bacteria) / Production host: Escherichia coli BL21 (bacteria) #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: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% PEG 3350, 200 mM lithium sulfate, 100 mM Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 46798 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.2→2.22 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2 / Num. unique obs: 1159 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.79 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9 / 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: 2.2→34.79 Å
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Refine LS restraints |
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LS refinement shell |
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