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- PDB-8ruj: 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: 8ruj | |||||||||||||||||||||||||||
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Title | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking | |||||||||||||||||||||||||||
![]() | 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 | ![]() | 451.2 KB | Display | ![]() |
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PDB format | ![]() | 363.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.4 KB | Display | ![]() |
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Full document | ![]() | 814.8 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8olsC ![]() 8olvC ![]() 8olwC ![]() 8olyC ![]() 8olzC ![]() 8om0C ![]() 8ruhC ![]() 8ruiC ![]() 8rukC ![]() 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: 126956.180 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-K / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.81 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 100 mM magnesium acetate, 200 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3% PEG8000 |
-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 11, 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: 3.12→49.52 Å / Num. obs: 35276 / % possible obs: 98.96 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.12→3.236 Å / Num. unique obs: 3419 / CC1/2: 0.316 |
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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: 147.217 Å2
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Refinement step | Cycle: 1 / Resolution: 3.12→49.52 Å
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Refine LS restraints |
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