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- PDB-7r8g: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r8g | ||||||
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Title | Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA | ||||||
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![]() | HYDROLASE/DNA / Argonaute / Ago / DNA guide / RNA cleavage / HYDROLASE-DNA complex | ||||||
Function / homology | nucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA / DNA (> 10) / Piwi domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, Y. / Murakami, K.S. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.9 KB | Display | ![]() |
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PDB format | ![]() | 133 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r8fC ![]() 7r8hC ![]() 7r8jC ![]() 7r8kC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 88038.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CVM52_05730 / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 5236.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.89 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 8.0, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.5→50 Å / Num. obs: 46475 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 75.05 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2292 / CC1/2: 0.344 / Rpim(I) all: 0.944 / Χ2: 1.16 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→44.86 Å
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Refine LS restraints |
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LS refinement shell |
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