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- PDB-3ho1: Crystal structure of T. thermophilus Argonaute N546 mutant protei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ho1 | ||||||
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Title | Crystal structure of T. thermophilus Argonaute N546 mutant protein complexed with DNA guide strand and 12-nt RNA target strand | ||||||
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![]() | NUCLEIC ACID BINDING PROTEIN/DNA/RNA / argonaute / protein-DNA-RNA complex / NUCLEIC ACID BINDING PROTEIN-DNA-RNA COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Li, H. / Sheng, G. / Patel, D.J. | ||||||
![]() | ![]() Title: Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Authors: Wang, Y. / Juranek, S. / Li, H. / Sheng, G. / Wardle, G.S. / Tuschl, T. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.2 KB | Display | ![]() |
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PDB format | ![]() | 121.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hjfC ![]() 3hk2C ![]() 3hm9C ![]() 3hvrC ![]() 3hxmC ![]() 3dlhS ![]() 3hge C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 76727.750 Da / Num. of mol.: 1 / Mutation: D546N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 3708.248 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, sitting drop / pH: 6 Details: containing 2.5 mM spermine, 10 mM MgCl2, 5 mM CaCl2, 50 mM Na cacodylate pH 6.0, 10% (v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 308 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 23588 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1155 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DLH Resolution: 2.6→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 36.035 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.85 Å2 / Biso mean: 61.367 Å2 / Biso min: 22.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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Xplor file |
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