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- PDB-5ceg: X-ray structure of toxin/anti-toxin complex from Mesorhizobium op... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ceg | ||||||
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Title | X-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum | ||||||
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![]() | TOXIN / Toxin Anti-toxin | ||||||
Function / homology | ![]() | ||||||
Biological species | Mesorhizobium opportunistum | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aakre, C.D. / Herrou, J. / Crosson, S. / Laub, M.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates. Authors: Aakre, C.D. / Herrou, J. / Phung, T.N. / Perchuk, B.S. / Crosson, S. / Laub, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.6 KB | Display | ![]() |
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Full document | ![]() | 464.9 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 10616.017 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5599 / Plasmid: pETDuet-1 / Details (production host): AmpR Production host: ![]() ![]() Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: F7YBW8 #2: Protein | Mass: 13490.321 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: His tagged protein Source: (gene. exp.) ![]() Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5598 / Plasmid: pETDuet-1 / Details (production host): AmpR Production host: ![]() ![]() Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: F7YBW7 |
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-Non-polymers , 4 types, 499 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.27 % / Description: spear-like crystals |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 400 mM Sodium Acetate, 100 mM Sodium Citrate pH5.5, 20% PEG 4000, 20 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→31.3 Å / Num. obs: 73683 / % possible obs: 99.95 % / Redundancy: 9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.59→1.63 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.59→29.71 Å
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Refine LS restraints |
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LS refinement shell |
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