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- PDB-2f8k: Sequence specific recognition of RNA hairpins by the SAM domain o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f8k | ||||||
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Title | Sequence specific recognition of RNA hairpins by the SAM domain of Vts1 | ||||||
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![]() | RNA BINDING PROTEIN/ RNA / VTS1-RNA complex / SAM domain / RNA BINDING PROTEIN- RNA COMPLEX | ||||||
Function / homology | ![]() flap-structured DNA binding / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of DNA metabolic process / nuclear-transcribed mRNA catabolic process / P-body / protein transport / nucleotide binding / mRNA binding / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Aviv, T. / Lin, Z. / Ben-Ari, G. / Smibert, C.A. / Sicheri, F. | ||||||
![]() | ![]() Title: Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Authors: Aviv, T. / Lin, Z. / Ben-Ari, G. / Smibert, C.A. / Sicheri, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.4 KB | Display | ![]() |
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PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2d3dS 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
#1: RNA chain | Mass: 5045.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SRE23 |
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#2: Protein | Mass: 10079.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VTS1 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.5 M Ammonium sulfate, 50 mM MES pH 5.5, 10 mM Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→64.55 Å / Num. obs: 11366 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.057 / Net I/σ(I): 11.37 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 6.43 / Num. unique all: 1523 / Rsym value: 0.139 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry: 2D3D Resolution: 2→64.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.102 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.185 / 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 | Biso mean: 26.027 Å2
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Refinement step | Cycle: LAST / Resolution: 2→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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