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Yorodumi- PDB-7r8j: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r8j | ||||||
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Title | Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' p guide DNA in the presence of Mg2+ | ||||||
Components |
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Keywords | HYDROLASE/DNA / argonaute / Ago / DNA guide / RNA cleavage / HYDROLASE-DNA complex | ||||||
Function / homology | nucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Piwi domain-containing protein Function and homology information | ||||||
Biological species | Pseudooceanicola lipolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Shin, Y. / Murakami, K.S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Authors: Lisitskaya, L. / Shin, Y. / Agapov, A. / Olina, A. / Kropocheva, E. / Ryazansky, S. / Aravin, A.A. / Esyunina, D. / Murakami, K.S. / Kulbachinskiy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r8j.cif.gz | 395.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r8j.ent.gz | 274.4 KB | Display | PDB format |
PDBx/mmJSON format | 7r8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/7r8j ftp://data.pdbj.org/pub/pdb/validation_reports/r8/7r8j | HTTPS FTP |
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-Related structure data
Related structure data | 7r8fC 7r8gC 7r8hC 7r8kC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 87914.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudooceanicola lipolyticus (bacteria) Gene: CVM52_05730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2M8J4C7 |
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#2: DNA/RNA hybrid | Mass: 5540.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudooceanicola lipolyticus (bacteria) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.72 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl, pH 8.0, 8% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 36116 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 80.77 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.037 / Χ2: 1.119 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1764 / CC1/2: 0.371 / Χ2: 1.134 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→44.54 Å / SU ML: 0.4215 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6956 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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