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- PDB-5xpg: Crystal structure of T. thermophilus Argonaute protein complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xpg | ||||||
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Title | Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target 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, J.D. / Wang, Y. | ||||||
![]() | ![]() 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 | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 127.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.8 KB | Display | ![]() |
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Full document | ![]() | 504.4 KB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xouC ![]() 5xowC ![]() 5xp8C ![]() 5xpaC ![]() 5xq2C ![]() 3dlhS 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 / DNA chain / RNA chain , 3 types, 3 molecules ACG
#1: Protein | Mass: 76727.750 Da / Num. of mol.: 1 / Mutation: D546N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0026 / Plasmid: PET-SUMO / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: RNA chain | Mass: 6271.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 26 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.09 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.0 M (NH4)2SO4, 0.1 M KCL, 10 MM MGCL2, 50 MM BIS-TRIS PH 6.5 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 308K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35223 / % possible obs: 99.5 % / Redundancy: 8.7 % / Biso Wilson estimate: 53.86 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DLH Resolution: 2.8→49.08 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.16
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Solvent computation | Bsol: 43.9 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→49.08 Å
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Refine LS restraints |
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LS refinement shell |
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