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Open data
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Basic information
Entry | Database: PDB / ID: 7c48 | |||||||||
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Title | Crystal structure of phosphorylated Ser78 form of Rv1045 toxin | |||||||||
![]() | Rv1045 toxin | |||||||||
![]() | TRANSFERASE / Nucleotidyltransferase / Toxin-Antitoxin / TglT Toxin / Rv1045 / guanylyltransferase | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Deep, A. / Kaur, J. / Thakur, K.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Rv1045 toxin in it's Ser78 phosphorylated form Authors: Deep, A. / Kaur, J. / Thakur, K.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.5 KB | Display | ![]() |
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PDB format | ![]() | 107.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7c46S S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 32077.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Rv1045 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4M ammonium phosphate dibasic, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→81.77 Å / Num. obs: 42300 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Rrim(I) all: 0.092 / Net I/σ(I): 24.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C46 Resolution: 1.6→81.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.748 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.181 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→81.77 Å
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Refine LS restraints |
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