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Yorodumi- PDB-3hvr: Crystal structure of T. thermophilus Argonaute complexed with DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hvr | ||||||
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Title | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | ||||||
Components |
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Keywords | NUCLEIC ACID BINDING PROTEIN/DNA/RNA / argonaute / protein-DNA-RNA complex / NUCLEIC ACID BINDING PROTEIN-DNA-RNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.211 Å | ||||||
Authors | Wang, Y. / Li, H. / Sheng, G. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hvr.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hvr.ent.gz | 220.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hvr_validation.pdf.gz | 502.4 KB | Display | wwPDB validaton report |
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Full document | 3hvr_full_validation.pdf.gz | 543.1 KB | Display | |
Data in XML | 3hvr_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 3hvr_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/3hvr ftp://data.pdbj.org/pub/pdb/validation_reports/hv/3hvr | HTTPS FTP |
-Related structure data
Related structure data | 3hjfC 3hk2SC 3hm9C 3ho1C 3hxmC 3hge C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 76728.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_P0026 / Plasmid: PET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3)pLysS / References: UniProt: Q746M7 #2: DNA chain | Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: RNA chain | Mass: 5942.584 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-MG / #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 34970 / % possible obs: 95.2 % / Observed criterion σ(F): -1 / Redundancy: 4.9 % / Biso Wilson estimate: 95.75 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3220 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HK2 Resolution: 3.211→37.68 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU ML: 0.51 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0.13 / 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 / Bsol: 68.32 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 293.57 Å2 / Biso mean: 97.522 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.211→37.68 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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