+Open data
-Basic information
Entry | Database: PDB / ID: 3i5x | ||||||
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Title | Structure of Mss116p bound to ssRNA and AMP-PNP | ||||||
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 / SIRAS / Resolution: 1.9 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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and preliminary X-ray diffraction of the DEAD-box protein Mss116p complexed with an RNA oligonucleotide and AMP-PNP 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 | 3i5x.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i5x.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 3i5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i5x ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i5x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) 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 |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: 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: 46.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M succinate, 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91842 Å |
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: 1.9→35 Å / Num. all: 48438 / Num. obs: 48438 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.9 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.9→34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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