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- PDB-2ply: Structure of the mRNA binding fragment of elongation factor SelB ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ply | ||||||
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Title | Structure of the mRNA binding fragment of elongation factor SelB in complex with SECIS RNA. | ||||||
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![]() | translation/RNA / protein-rna / complex / rna / winged helix / selb / SECIS / translation-RNA COMPLEX | ||||||
Function / homology | ![]() selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soler, N. / Fourmy, D. / Yoshizawa, S. | ||||||
![]() | ![]() Title: Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. Authors: Soler, N. / Fourmy, D. / Yoshizawa, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA Authors: Soler, N. / Fourmy, D. / Yoshizawa, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.5 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.6 KB | Display | ![]() |
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Full document | ![]() | 504.1 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pjpC ![]() 1lvaS ![]() 1wsuS 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
-RNA chain / Protein , 2 types, 4 molecules CEAB
#1: RNA chain | Mass: 7386.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcription #2: Protein | Mass: 29741.746 Da / Num. of mol.: 2 / Mutation: S535W, F536V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 133 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
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![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG4000, 0.1M Na-Acetate pH 4.6, 0.2M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2003 |
Radiation | Monochromator: 2mirrors: N2 cooled + sagittaly bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→95.563 Å / Num. all: 27498 / Num. obs: 28977 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.517 / % possible all: 100 |
-Phasing
Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WSU,1LVA Resolution: 2.6→95.35 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.84 / SU B: 9.5 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.313 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.325 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→95.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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