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Yorodumi- PDB-4e8k: Structure of Oceanobacillus iheyensis group II intron in the pres... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e8k | ||||||
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Title | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | ||||||
Components |
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Keywords | RNA / ribozyme / 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: 3.03 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 | 4e8k.cif.gz | 450.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8k.ent.gz | 362.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8k ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8k | HTTPS FTP |
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-Related structure data
Related structure data | 4e8mC 4e8nC 4e8pC 4e8qC 4e8rC 4e8tC 4e8vC 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 , 2 types, 2 molecules AB
#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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#2: RNA chain | Mass: 3123.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide fragment |
-Non-polymers , 5 types, 85 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-EPE / #6: Chemical | ChemComp-SPM / | #7: 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: 3.64 Å3/Da / Density % sol: 66.23 % |
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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, 100 mM calcium chloride, 50 mM HEPES sodium, pH 7.0, 5% 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-E / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2011 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→50 Å / Num. obs: 32515 / % possible obs: 92 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3.03→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.7 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IGI Resolution: 3.03→49.11 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.939 / SU B: 32.961 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 103.849 Å2
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Refinement step | Cycle: LAST / Resolution: 3.03→49.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.033→3.112 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 25.211 Å / Origin y: 8.997 Å / Origin z: 25.273 Å
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