+Open data
-Basic information
Entry | Database: PDB / ID: 4tyn | ||||||
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Title | DEAD-box helicase Mss116 bound to ssDNA and ADP-BeF | ||||||
Components |
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Keywords | HYDROLASE/DNA / DEAD-box / RNA helicase / hydrolase / RNA BINDING PROTEIN-DNA complex / HYDROLASE-DNA 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: 2.959 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 | 4tyn.cif.gz | 200.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tyn.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tyn_validation.pdf.gz | 800.6 KB | Display | wwPDB validaton report |
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Full document | 4tyn_full_validation.pdf.gz | 804.3 KB | Display | |
Data in XML | 4tyn_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4tyn_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/4tyn ftp://data.pdbj.org/pub/pdb/validation_reports/ty/4tyn | HTTPS FTP |
-Related structure data
Related structure data | 4tywC 4tyyC 4tz0C 4tz6C 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: DNA chain | Mass: 2147.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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#2: 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 (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P15424, RNA helicase |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-BEF / |
#5: Chemical | ChemComp-ADP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium acetate, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 77 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: Mar 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.959→44.15 Å / Num. obs: 13129 / % possible obs: 94.64 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 8.55 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.46 / Rsym value: 0.491 / % possible all: 88 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1583) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I5X Resolution: 2.959→44.15 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / 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: 2.959→44.15 Å
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Refine LS restraints |
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LS refinement shell |
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