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- PDB-6j7r: Crystal structure of toxin TglT (unusual type guanylyltransferase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j7r | |||||||||
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Title | Crystal structure of toxin TglT (unusual type guanylyltransferase-like toxin, Rv1045) mutant S78A co-expressed with TakA from Mycobacterium tuberculosis | |||||||||
![]() | guanylyltransferase-like toxin | |||||||||
![]() | TOXIN / guanylyltransferase / guanylyltransferase-like toxin / TA | |||||||||
Function / homology | Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / metal ion binding / Nucleotidyl transferase AbiEii/AbiGii toxin family protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yu, X. / Gao, X. / Zhu, K. / Wojdyla, J.A. / Wang, M. / Cui, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism. Authors: Yu, X. / Gao, X. / Zhu, K. / Yin, H. / Mao, X. / Wojdyla, J.A. / Qin, B. / Huang, H. / Wang, M. / Sun, Y.C. / Cui, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.4 KB | Display | ![]() |
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PDB format | ![]() | 92.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.9 KB | Display | ![]() |
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Full document | ![]() | 434.7 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j7nC ![]() 6j7oC ![]() 6j7pC ![]() 6j7qC ![]() 6j7sC ![]() 6j7tSC S: Starting model for refinement C: citing same article ( |
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Similar 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: 34185.023 Da / Num. of mol.: 1 / Mutation: S78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: Rv1045 / Plasmid: pet28a / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 0.2 M magnesium chloride hexahydrate, 25% polyethylene glycol 3350 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: May 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→47.824 Å / Num. obs: 15853 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4.55 % / Biso Wilson estimate: 56.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.69 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 4.65 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 2558 / CC1/2: 0.825 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J7T Resolution: 2.299→47.824 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.299→47.824 Å
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Refine LS restraints |
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LS refinement shell |
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