[English] 日本語
![](img/lk-miru.gif)
- PDB-1euj: A NOVEL ANTI-TUMOR CYTOKINE CONTAINS A RNA-BINDING MOTIF PRESENT ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1euj | ||||||
---|---|---|---|---|---|---|---|
Title | A NOVEL ANTI-TUMOR CYTOKINE CONTAINS A RNA-BINDING MOTIF PRESENT IN AMINOACYL-TRNA SYNTHETASES | ||||||
![]() | ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2 | ||||||
![]() | CYTOKINE / EMAP 2 / EMAP II / tRNA synthetase / apoptosis / RNA binding motif | ||||||
Function / homology | ![]() positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling ...positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling / angiogenesis / defense response to virus / tRNA binding / inflammatory response / translation / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Kim, Y. / Shin, J. / Li, R. / Cheong, C. / Kim, S. | ||||||
![]() | ![]() Title: A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases. Authors: Kim, Y. / Shin, J. / Li, R. / Cheong, C. / Kim, K. / Kim, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer in vivo, but forms a dimer in a asymmetric unit in crystal by the two-fold. |
-
Components
#1: Protein | Mass: 18242.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% PEG 4000, 100 mM NaAcetate, 15 mM MgCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 21K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 35728 / Num. obs: 31502 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.8 / Redundancy: 3.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.282 / % possible all: 37.9 |
Reflection | *PLUS Num. measured all: 96335 |
Reflection shell | *PLUS % possible obs: 37.9 % / Mean I/σ(I) obs: 1.8 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.7 Å2 |