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- PDB-6t3r: Structure of Oceanobacillus iheyensis group II intron U-mutant (C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t3r | ||||||||||||
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Title | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon | ||||||||||||
![]() | (Group IIC Intron ...) x 2 | ||||||||||||
![]() | RNA / Ribozyme / Self-splicing / Retrotransposition / Spliceosome | ||||||||||||
Function / homology | : / SPERMINE / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Marcia, M. / Pyle, A.M. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Visualizing group II intron dynamics between the first and second steps of splicing. Authors: Manigrasso, J. / Chillon, I. / Genna, V. / Vidossich, P. / Somarowthu, S. / Pyle, A.M. / 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 | ![]() | 239.4 KB | Display | ![]() |
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PDB format | ![]() | 178.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t3kC ![]() 6t3nC ![]() 6t3sC ![]() 3igiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Group IIC Intron ... , 2 types, 2 molecules AB
#1: RNA chain | Mass: 126596.945 Da / Num. of mol.: 1 / Fragment: domains 1-5 / Mutation: C289U/C358U/G385A / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) ![]() |
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#2: RNA chain | Mass: 2583.569 Da / Num. of mol.: 1 / Fragment: 5'-exon / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) ![]() |
-Non-polymers , 5 types, 105 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.41 % / Mosaicity: 0.46 ° |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM Na-HEPES pH 7.0, 100 mM magnesium acetate, 150 mM potassium chloride, 10 mM lithium chloride, 4% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL SI(220) SIDE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.567→44.48 Å / Num. all: 22945 / Num. obs: 22945 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.157 / Rsym value: 0.13 / Net I/av σ(I): 4.6 / Net I/σ(I): 9.4 / Num. measured all: 108124 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IGI Resolution: 3.57→34.85 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 328.26 Å2 / Biso mean: 122.1935 Å2 / Biso min: 50.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.57→34.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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