[English] 日本語
![](img/lk-miru.gif)
- PDB-4ohy: C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ohy | ||||||
---|---|---|---|---|---|---|---|
Title | C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state) | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN/RNA / polynucleotide kinase / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() Processing of Capped Intron-Containing Pre-mRNA / Processing of Intronless Pre-mRNAs / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / : / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dikfidan, A. / Loll, B. / Zeymer, C. / Clausen, T. / Meinhart, A. | ||||||
![]() | ![]() Title: RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1. Authors: Dikfidan, A. / Loll, B. / Zeymer, C. / Magler, I. / Clausen, T. / Meinhart, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 181.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 141.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1018.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ohvC ![]() 4ohwC ![]() 4ohxC ![]() 4ohzC ![]() 4oi0C ![]() 4oi1C ![]() 4oi2C ![]() 4oi4C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 47936.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: RNA chain | Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized |
-Non-polymers , 4 types, 152 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ANP / |
---|---|
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-2PE / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Na2HPO4/KH2PO4 200 mM NaCl 15 mM MgCl2 90 mM sarcosine 25% (w/v) PEG 1000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 30691 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 42.1 Å2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.1 % / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.148 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|