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Open data
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Basic information
Entry | Database: PDB / ID: 8s4t | ||||||||||||
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Title | DNA bound structure of PrgE from plasmid pCF10 | ||||||||||||
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![]() | DNA BINDING PROTEIN / SSB | ||||||||||||
Function / homology | TRIETHYLENE GLYCOL / DNA / DNA (> 10) / PrgE![]() | ||||||||||||
Biological species | ![]() ![]() DNA molecule (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Breidenstein, A. / Berntsson, R.P.-A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: ssDNA-binding protein PrgE and its role in Enterococcal conjugation Authors: Breidenstein, A. / Lamy, A. / Bader, C.P.J. / Sung, W. / Wanrooij, P.H. / Berntsson, R.P.-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 | ![]() | 199.5 KB | Display | ![]() |
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PDB format | ![]() | 159.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s4sC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 17067.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: prgK, prgE, EGX33_13060, EU507_13905, F6H88_002583, FDO46_002730, H9Q64_07920, HRF81_13830, IHC34_002761, KCT30_002803, NAG05_14735 Production host: ![]() ![]() #2: DNA chain | | Mass: 18747.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15 % Polyethylene glycol 400, 50 mM MES pH 6.5, 80 mM Magnesium acetate, 15 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→49.74 Å / Num. obs: 26266 / % possible obs: 99.75 % / Redundancy: 6.7 % / Biso Wilson estimate: 73.16 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.1158 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 2.67→2.765 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2536 / CC1/2: 0.628 / Rrim(I) all: 2.067 / % possible all: 99.06 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 94.065 Å2
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Refinement step | Cycle: 1 / Resolution: 2.67→49.74 Å
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