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Open data
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Basic information
Entry | Database: PDB / ID: 6gto | ||||||
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Title | Structure of the AtaR antitoxin | ||||||
![]() | DUF1778 domain-containing protein | ||||||
![]() | TRANSCRIPTION / antitoxin / transcription factor / ribbon-helix-helix / RHH / bacterial repressor | ||||||
Function / homology | Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / toxin sequestering activity / Ribbon-helix-helix / regulation of DNA-templated transcription / DUF1778 domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Pino, A. / Jurenas, D. | ||||||
![]() | ![]() Title: Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system. Authors: Jurenas, D. / Van Melderen, L. / Garcia-Pino, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38 KB | Display | ![]() |
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PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.8 KB | Display | ![]() |
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Full document | ![]() | 409.8 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 4.9 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9925.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_ ...Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_07330, BMT53_16880, BN17_33961, BTQ04_07040, BWP17_00645, COD46_18440, CR538_01655, CVH05_12360, ERS085366_00076, ERS085374_01548, ERS085383_01733, ERS085404_01502, RX35_03224 Production host: ![]() ![]() References: UniProt: J7QA90 |
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#2: Chemical | ChemComp-NA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35%(v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→41.86 Å / Num. obs: 3575 / % possible obs: 99.61 % / Redundancy: 5.5 % / Biso Wilson estimate: 117.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.58 |
Reflection shell | Resolution: 2.97→3.08 Å / Rmerge(I) obs: 1.482 / CC1/2: 0.538 / % possible all: 99.42 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 134.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.97→41.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.97→3.32 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 27.1228 Å / Origin y: 19.2179 Å / Origin z: 75.0485 Å
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Refinement TLS group | Selection details: { A|* } |