+Open data
-Basic information
Entry | Database: PDB / ID: 3i61 | ||||||
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Title | Structure of Mss116p bound to ssRNA and ADP-Beryllium Fluoride | ||||||
Components |
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Keywords | 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 | Function and homology information Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / RNA helicase activity / RNA helicase ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / RNA helicase activity / RNA helicase / mitochondrial matrix / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Del Campo, M. / Lambowitz, A.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i61.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i61.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i61_validation.pdf.gz | 815.3 KB | Display | wwPDB validaton report |
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Full document | 3i61_full_validation.pdf.gz | 818.6 KB | Display | |
Data in XML | 3i61_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3i61_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i61 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i61 | HTTPS FTP |
-Related structure data
Related structure data | 3i5xSC 3i5yC 3i62C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 2 molecules AB
#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.) Saccharomyces cerevisiae (brewer's yeast) Gene: MSS116, YD9346.05C, YDR194C / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P15424, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: RNA chain | Mass: 3016.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA fragment commercially available |
-Non-polymers , 4 types, 221 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-BEF / |
#5: Chemical | ChemComp-MG / |
#6: 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: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% tacsimate, 15% PEG 3350, 2.5% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. all: 36177 / Num. obs: 36177 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.5 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3I5X Resolution: 2.1→33.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.172 / 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: 2.1→33.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.103→2.158 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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