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Yorodumi- PDB-8oly: Structure of Oceanobacillus iheyensis group II intron post first ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oly | |||||||||||||||||||||||||||
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Title | Structure of Oceanobacillus iheyensis group II intron post first step of splicing in the presence of K+, Mg2+ and intronistat B | |||||||||||||||||||||||||||
Components |
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Keywords | RNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION | |||||||||||||||||||||||||||
Function / homology | : / SPERMINE / RNA / RNA (> 10) / RNA (> 100) Function and homology information | |||||||||||||||||||||||||||
Biological species | Oceanobacillus iheyensis (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å | |||||||||||||||||||||||||||
Authors | Silvestri, I. / Marcia, M. | |||||||||||||||||||||||||||
Funding support | France, Italy, 8items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oly.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oly.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 8oly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oly_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 8oly_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 8oly_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 8oly_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/8oly ftp://data.pdbj.org/pub/pdb/validation_reports/ol/8oly | HTTPS FTP |
-Related structure data
Related structure data | 8olsC 8olvC 8olwC 8olzC 8om0C 8ruhC 8ruiC 8rujC 8rukC 8rulC 8rumC 8runC 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
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 126956.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria) |
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#2: RNA chain | Mass: 1547.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria) |
-Non-polymers , 5 types, 105 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-EPE / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.15 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 100 mM magnesium acetate, 100 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3.5% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.02 Å / Num. obs: 34101 / % possible obs: 98.69 % / Redundancy: 4.2 % / CC1/2: 1 / Net I/σ(I): 10.57 |
Reflection shell | Resolution: 3.1→3.2 Å / Num. unique obs: 3245 / CC1/2: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→48.02 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 23.462 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 |
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Refinement step | Cycle: 1 / Resolution: 3.11→48.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.111→3.192 Å / Total num. of bins used: 20
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