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Yorodumi- PDB-1u04: Crystal structure of full length Argonaute from Pyrococcus furiosus -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u04 | ||||||
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Title | Crystal structure of full length Argonaute from Pyrococcus furiosus | ||||||
Components | hypothetical protein PF0537Hypothesis | ||||||
Keywords | HYDROLASE/GENE REGULATION / RNAi / Silencing / Argonaute / PIWI / PAZ / RISC / Slicer / RNase H / HYDROLASE-GENE REGULATION 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 binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | Song, J.J. / Smith, S.K. / Hannon, G.J. / Joshua-Tor, L. | ||||||
Citation | Journal: Science / Year: 2004 Title: Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity Authors: Song, J.J. / Smith, S.K. / Hannon, G.J. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u04.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u04.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u04 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u04 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 91441.305 Da / Num. of mol.: 1 / Mutation: K4I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIPL / References: UniProt: Q8U3D2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 290 K / pH: 8 Details: alcohol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 8.00 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.979036 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.25→38.17 Å / Num. obs: 48822 / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.1 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 2.25→2.39 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→38.17 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1695436.78 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.1711 Å2 / ksol: 0.327326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→38.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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