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- PDB-3i5y: Structure of Mss116p bound to ssRNA containing a single 5-BrU and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i5y | ||||||
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Title | Structure of Mss116p bound to ssRNA containing a single 5-BrU and AMP-PNP | ||||||
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![]() | Hydrolase/RNA / Protein-RNA complex / RNA helicase / DEAD-box / ATP-binding / Helicase / Hydrolase / Mitochondrion / mRNA processing / mRNA splicing / Nucleotide-binding / RNA-binding / Transit peptide / Translation regulation / Hydrolase-RNA COMPLEX | ||||||
Function / homology | ![]() transcription elongation by mitochondrial RNA polymerase / Group II intron splicing / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / regulation of translation / RNA helicase activity ...transcription elongation by mitochondrial RNA polymerase / Group II intron splicing / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / regulation of translation / RNA helicase activity / RNA helicase / mitochondrial matrix / mRNA binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Del Campo, M. / Lambowitz, A.M. | ||||||
![]() | ![]() Title: Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA Authors: Del Campo, M. / Lambowitz, A.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 | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 91.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.3 KB | Display | ![]() |
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Full document | ![]() | 795 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i5xSC ![]() 3i61C ![]() 3i62C S: Starting model for refinement C: citing same article ( |
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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: Protein | Mass: 64483.715 Da / Num. of mol.: 1 / Fragment: UNP residues 37 to 597 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MSS116, YD9346.05C, YDR194C / Plasmid: pMAL / Production host: ![]() ![]() References: UniProt: P15424, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: RNA chain | Mass: 3095.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA fragment commercially available |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% tacsimate, 15% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→35 Å / Num. all: 21524 / Num. obs: 21524 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.5 / % possible all: 75.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3I5X Resolution: 2.49→34.88 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.603 / ESU R Free: 0.287 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→34.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.494→2.559 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 |
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