+Open data
-Basic information
Entry | Database: PDB / ID: 4tz6 | ||||||
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Title | DEAD-box helicase Mss116 bound to ssRNA and UDP-BeF | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / DEAD-box / RNA helicase / hydrolase / RNA binding protein-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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / regulation of translation / RNA helicase activity ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å | ||||||
Authors | Mallam, A.L. / Sidote, D.J. / Lambowitz, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2014 Title: Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase. Authors: Mallam, A.L. / 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 | 4tz6.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tz6.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 4tz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/4tz6 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tz6 | HTTPS FTP |
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-Related structure data
Related structure data | 4tynC 4tywC 4tyyC 4tz0C 3i5xS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57843.730 Da / Num. of mol.: 1 / Fragment: UNP residues 88-596 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / References: UniProt: P15424, RNA helicase |
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#2: RNA chain | Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: Chemical | ChemComp-BEF / |
#4: Chemical | ChemComp-UDP / |
#5: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M DL-malic acid, pH 7.0, 12 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.209→47.211 Å / Num. obs: 10514 / % possible obs: 96.72 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.209→3.36 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.5 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I5X Resolution: 3.209→47.211 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.209→47.211 Å
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Refine LS restraints |
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LS refinement shell |
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