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- PDB-8ruk: Structure of Oceanobacillus iheyensis group II intron in the pres... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ruk | |||||||||||||||||||||||||||
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Title | Structure of Oceanobacillus iheyensis group II intron in the presence of Na+, Mg2+, and ARN25850 | |||||||||||||||||||||||||||
![]() | Domains 1-5 | |||||||||||||||||||||||||||
![]() | RNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION | |||||||||||||||||||||||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Silvestri, I. / Marcia, M. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Targeting the conserved active site of splicing machines with specific and selective small molecule modulators. Authors: Silvestri, I. / Manigrasso, J. / Andreani, A. / Brindani, N. / Mas, C. / Reiser, J.B. / Vidossich, P. / Martino, G. / McCarthy, A.A. / De Vivo, M. / Marcia, M. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 443.3 KB | Display | ![]() |
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PDB format | ![]() | 357.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 670 KB | Display | ![]() |
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Full document | ![]() | 699.9 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8olsC ![]() 8olvC ![]() 8olwC ![]() 8olyC ![]() 8olzC ![]() 8om0C ![]() 8ruhC ![]() 8ruiC ![]() 8rujC ![]() 8rulC ![]() 8rumC ![]() 8runC 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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1 |
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Unit cell |
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Components
#1: RNA chain | Mass: 127991.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
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#2: Chemical | ChemComp-VTR / Mass: 568.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20Br2N2O6 / Feature type: SUBJECT OF INVESTIGATION | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.97 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 100 mM Mg-Acetate, 150 mM NaCl, 50 mM Na-HEPES pH 7.0, 3%PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 4.81→48.55 Å / Num. obs: 9771 / % possible obs: 99.79 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1403 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 4.81→4.982 Å / Num. unique obs: 947 / CC1/2: 0.787 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 168.148 Å2
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Refinement step | Cycle: 1 / Resolution: 4.81→48.55 Å
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Refine LS restraints |
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