+
Open data
-
Basic information
Entry | Database: PDB / ID: 4tyw | ||||||
---|---|---|---|---|---|---|---|
Title | DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN/RNA / DEAD-box / ![]() ![]() | ||||||
Function / homology | ![]() 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) / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mallam, A.L. / Sidote, D.J. / Lambowitz, A.M. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 208.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 165.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4tynC ![]() 4tyyC ![]() 4tz0C ![]() 4tz6C ![]() 3i5xS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 57785.699 Da / Num. of mol.: 1 / Fragment: UNP residues 88-595 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: ![]() ![]() ![]() ![]() |
---|---|
#2: RNA chain | Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 119 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-BEF / | #5: Chemical | ChemComp-ADP / | ![]() #6: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.11 % |
---|---|
Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, pH 7.5, 2 % tacsimate pH 7.0, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.197→47.243 Å / Num. obs: 32642 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.54 / Rsym value: 0.444 / % possible all: 97.7 |
-
Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 3I5X Resolution: 2.197→47.243 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.65 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.197→47.243 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|