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- PDB-1ryn: Structure of the Chloroplast Group II Intron Splicing Factor CRS2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ryn | ||||||
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Title | Structure of the Chloroplast Group II Intron Splicing Factor CRS2 | ||||||
![]() | protein CRS2 | ||||||
![]() | TRANSLATION / ALPHA-BETA | ||||||
Function / homology | ![]() aminoacyl-tRNA hydrolase activity / chloroplast stroma / RNA splicing / mRNA processing / ribonucleoprotein complex Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ostheimer, G.J. / Barkan, A. / Matthews, B.W. | ||||||
![]() | ![]() Title: Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces Authors: Ostheimer, G.J. / Hadjivasiliou, H. / Kloer, D.P. / Barkan, A. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.5 KB | Display | ![]() |
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Full document | ![]() | 428.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 22552.658 Da / Num. of mol.: 1 / Fragment: CRS2(NFT) / Mutation: I42N, S44F, I50T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 30% PEG 4000, lithium sulfate, Tris, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.75→15 Å / Num. all: 16370 / Num. obs: 14897 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2216 / Rsym value: 0.246 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 14925 / % possible obs: 92.3 % / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.246 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CRS2 through K178 Resolution: 1.75→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: bulk solvent modelled with TNT / Bsol: 109 Å2 / ksol: 0.85 e/Å3 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.199 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.7 |