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Yorodumi- PDB-2d3d: crystal structure of the RNA binding SAM domain of saccharomyces ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d3d | ||||||
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Title | crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1 | ||||||
Components | Vts1 protein | ||||||
Keywords | RNA BINDING PROTEIN / RNA binding / SAM domain / SRE hairpin binding | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.6 Å | ||||||
Authors | Aviv, T. / Amborski, A.N. / Zhao, X.S. / Kwan, J.J. / Johnson, P.E. / Sicheri, F. / Donaldson, L.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The NMR and X-ray Structures of the Saccharomyces cerevisiae Vts1 SAM Domain Define a Surface for the Recognition of RNA Hairpins Authors: Aviv, T. / Amborski, A.N. / Zhao, X.S. / Kwan, J.J. / Johnson, P.E. / Sicheri, F. / Donaldson, L.W. #1: Journal: Nat.Struct.Biol. / Year: 2003 Title: The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators Authors: Aviv, T. / Lin, Z. / Lau, S. / Rendl, L.M. / Sicheri, F. / Smibert, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d3d.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d3d.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 2d3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/2d3d ftp://data.pdbj.org/pub/pdb/validation_reports/d3/2d3d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10079.785 Da / Num. of mol.: 1 / Fragment: minimal RNA binding fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Vts1 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 6324935, UniProt: Q08831*PLUS |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, ammonium chloride, calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26.6 Å / Num. all: 10544 / Num. obs: 9742 / % possible obs: 92.4 % / Observed criterion σ(F): 3 / Redundancy: 5.1 % / Rsym value: 0.038 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 960 / Rsym value: 0.184 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.6→26.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.351 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.191 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.955 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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