[English] 日本語
![](img/lk-miru.gif)
- PDB-5n2v: Changes in conformational equilibria regulate the activity of the... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5n2v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme | |||||||||
![]() |
| |||||||||
![]() | RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / mRNA cap binding ...mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / mRNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / mRNA binding / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Holdermann, I. / Sprangers, R. | |||||||||
Funding support | 1items
| |||||||||
![]() | ![]() Title: Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Authors: Wurm, J.P. / Holdermann, I. / Overbeck, J.H. / Mayer, P.H.O. / Sprangers, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 166.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j3tS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15130.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dcp1, SPBC3B9.21 / Production host: ![]() ![]() #2: Protein | Mass: 28689.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dcp2, SPAC19A8.12 / Production host: ![]() ![]() #3: Protein/peptide | Mass: 2742.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Chemical | ChemComp-MG / #5: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 41% M1K3350 Morpheus Mix 4, MOPS pH 7.0, 0.06 M MgCl2/CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.3 Å / Num. obs: 15440 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.95 / Rmerge(I) obs: 0.24 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.64 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5j3t Resolution: 3.1→48.289 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.289 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|