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Yorodumi- PDB-4e8v: Structure of Oceanobacillus iheyensis group II intron in a ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e8v | ||||||
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Title | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+ | ||||||
Components | Group IIC intron | ||||||
Keywords | RNA / ribozyme / metalloenzyme / self-splicing / retrotransposition | ||||||
Function / homology | : / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Oceanobacillus iheyensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.995 Å | ||||||
Authors | Marcia, M. / Pyle, A.M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Visualizing Group II Intron Catalysis through the Stages of Splicing. Authors: Marcia, M. / Pyle, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e8v.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8v.ent.gz | 174.8 KB | Display | PDB format |
PDBx/mmJSON format | 4e8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8v ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8v | HTTPS FTP |
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-Related structure data
Related structure data | 4e8kC 4e8mC 4e8nC 4e8pC 4e8qC 4e8rC 4e8tC 4faqC 4farC 4fauC 4fawC 4faxC 4fb0C 3igiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 127646.586 Da / Num. of mol.: 1 / Fragment: domains 1-5 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Oceanobacillus iheyensis (bacteria) |
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-Non-polymers , 5 types, 86 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-BA / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-EPE / #6: Water | ChemComp-HOH / | |
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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: 3.82 Å3/Da / Density % sol: 67.8 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM potassium acetate, 100 mM potassium chloride, 150 mM barium chloride, 50 mM HEPES sodium, pH 7.0, 6% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.485 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.485 Å / Relative weight: 1 |
Reflection | Resolution: 3.99→113.837 Å / Num. obs: 16781 / % possible obs: 98.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.99→4.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 1.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IGI Resolution: 3.995→47.908 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 39.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.995→47.908 Å
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Refine LS restraints |
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LS refinement shell |
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