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Yorodumi- PDB-4db4: Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4db4 | ||||||
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Title | Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex | ||||||
Components |
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Keywords | RNA-BINDING PROTEIN/DNA / RNA / DEAD-box / RNA helicase / hydrolase / RNA-BINDING PROTEIN-DNA / 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: 3.599 Å | ||||||
Authors | Mallam, A.L. / Del Campo, M. / Gilman, B.D. / Sidote, D.J. / Lambowitz, A. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p. Authors: Mallam, A.L. / Del Campo, M. / Gilman, B. / Sidote, D.J. / 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 | 4db4.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4db4.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 4db4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/4db4 ftp://data.pdbj.org/pub/pdb/validation_reports/db/4db4 | HTTPS FTP |
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-Related structure data
Related structure data | 4db2C 3i5xS 4dax 4daz C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 29127.637 Da / Num. of mol.: 2 / Fragment: Domain 2 (UNP residues 342-596) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MSS116, YDR194C, YD9346.05C / Organelle: mitochondrion / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P15424, RNA helicase #2: DNA/RNA hybrid | Mass: 4395.755 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 6% tacsimate, pH 5.0, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2011 |
Radiation | Monochromator: Double-crystal Si(111), liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 3.599→50 Å / Num. obs: 8213 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.599→3.66 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I5X Resolution: 3.599→42.818 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 27.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.054 Å2 / ksol: 0.27 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.599→42.818 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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