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- PDB-5xq2: Crystal structure of T. thermophilus Argonaute protein complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xq2 | |||||||||||||||
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Title | Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand | |||||||||||||||
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![]() | DNA BINDING PROTEIN / Argonaute / miRNA / bulge / mismatch | |||||||||||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Sheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D. / Wang, Y. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes Authors: Sheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D.J. / Wang, Y. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 592.4 KB | Display | ![]() |
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PDB format | ![]() | 485.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xouC ![]() 5xowC ![]() 5xp8C ![]() 5xpaC ![]() 5xpgC ![]() 4kpyS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 76727.750 Da / Num. of mol.: 2 / Mutation: D546N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0026 / Production host: ![]() ![]() |
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-DNA chain , 3 types, 6 molecules XEYFCD
#2: DNA chain | Mass: 6901.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | Mass: 5708.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: DNA chain | Mass: 901.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 2 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.61 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop Details: 2.8 M Na-acetate, pH7.0, 0.1M Tris-Cl, pH 8.0 and 0.15 M glycine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→50 Å / Num. obs: 40665 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 45.5 |
Reflection shell | Resolution: 3.32→3.38 Å / Redundancy: 26.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KPY Resolution: 3.33→48.95 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 28.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.33→48.95 Å
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Refine LS restraints |
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LS refinement shell |
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