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- PDB-6tuo: Crystal structure of Archaeoglobus fulgidus Argonaute protein wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tuo | ||||||
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Title | Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT | ||||||
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![]() | DNA BINDING PROTEIN / ARGONAUTE / PIWI DOMAIN / PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Grazulis, S. / Zaremba, M. | ||||||
![]() | ![]() Title: Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT Authors: Golovinas, E. / Manakova, E. / Sasnauskas, G. / Zaremba, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 95.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 475.8 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ytuS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / DNA chain , 2 types, 3 molecules ARS
#1: Protein | Mass: 50921.121 Da / Num. of mol.: 1 / Fragment: Arhaeoglobus fulgidus Argonaute protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 4304 / Gene: AF_1318 / Plasmid: pETDuet / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 4278.815 Da / Num. of mol.: 2 / Fragment: oligodeoxyribonucleotide / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 6 types, 360 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||||||
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#4: Chemical | ChemComp-CL / | ||||||
#5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Na-Cacodylate pH 5.5 0.05 M, KCl_0.2 M, MgCl2 0.01 M, PEG4000 5% (w/v), glycerol 5% (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2018 / Details: silica substrate + Rh coating | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Oxford-FMB, UK; Si(111) or Si(311); both crystals LN2 cooled, fixed exit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→99.63 Å / Num. all: 349485 / Num. obs: 53664 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 20.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | R rigid body: 0.461
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 1ytu Resolution: 1.8→54.901 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 27.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.13 Å2 / Biso mean: 48.285 Å2 / Biso min: 15.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→54.901 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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