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Open data
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Basic information
Entry | Database: PDB / ID: 6ifm | |||||||||
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Title | Crystal structure of DNA bound VapBC from Salmonella typhimurium | |||||||||
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![]() | TOXIN/ANTITOXIN/DNA / Toxin-Antitoxin / TOXIN-ANTITOXIN-DNA complex | |||||||||
Function / homology | ![]() RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Park, D.W. / Lee, B.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca2+-dependent ribonuclease. Authors: Park, D. / Yoon, H.J. / Lee, K.Y. / Park, S.J. / Cheon, S.H. / Lee, H.H. / Lee, S.J. / Lee, B.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.1 KB | Display | ![]() |
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PDB format | ![]() | 156.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.3 KB | Display | ![]() |
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Full document | ![]() | 515.4 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 49.1 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: 14957.292 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapC, STM3033 / Production host: ![]() ![]() References: UniProt: Q8ZM86, Hydrolases; Acting on ester bonds #2: Protein | Mass: 7677.576 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapB, STM3034 / Production host: ![]() ![]() #3: DNA chain | | Mass: 8176.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | | Mass: 8412.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium citrate tribasic pH7, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 29329 / % possible obs: 99 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.8→2.886 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 9280 / % possible all: 97.9 |
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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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.804→48.867 Å
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Refine LS restraints |
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LS refinement shell |
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