+
Open data
-
Basic information
Entry | Database: PDB / ID: 7o4e | ||||||
---|---|---|---|---|---|---|---|
Title | The DYW domain of A. thaliana OTP86 in its inactive state | ||||||
![]() | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic | ||||||
![]() | HYDROLASE / cytidine deaminase | ||||||
Function / homology | ![]() chloroplast RNA processing / RNA modification / chloroplast / mRNA processing / intracellular membrane-bounded organelle / mRNA binding / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weber, G. / Palm, G.J. / Takenaka, M. / Barthel, T. / Feiler, C. / Weiss, M.S. | ||||||
![]() | ![]() Title: DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis. Authors: Takenaka, M. / Takenaka, S. / Barthel, T. / Frink, B. / Haag, S. / Verbitskiy, D. / Oldenkott, B. / Schallenberg-Rudinger, M. / Feiler, C.G. / Weiss, M.S. / Palm, G.J. / Weber, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 67.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 16016.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 nl protein plus 100 nl reservoir (0.1 M glycine, pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4) plus 30 nl additive (0.1 M 50% v/v Jeffamine M-600 pH 7.0). Cryo: reservoir solution ...Details: 100 nl protein plus 100 nl reservoir (0.1 M glycine, pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4) plus 30 nl additive (0.1 M 50% v/v Jeffamine M-600 pH 7.0). Cryo: reservoir solution supplemented with 15% (v/v) ethylene glycol. PH range: 7.9 - 10.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→80 Å / Num. obs: 16019 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.3 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.235 / Rsym value: 0.216 / Net I/σ(I): 7.46 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1761 / CC1/2: 0.428 / Rrim(I) all: 1.899 / Rsym value: 1.734 / % possible all: 99 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: D_129211461 Resolution: 2.5→38.722 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.54 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 96.8 Å2 / Biso mean: 48.7795 Å2 / Biso min: 26.76 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→38.722 Å
| ||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|