+
Open data
-
Basic information
Entry | Database: PDB / ID: 3hb0 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of edeya2 complexed with bef3 | ||||||
![]() | Eyes absent homolog 2 (Drosophila) | ||||||
![]() | HYDROLASE / alpha/beta hydrolase | ||||||
Function / homology | ![]() histone H2AXY142 phosphatase activity / mesodermal cell fate specification / anatomical structure development / striated muscle tissue development / mitochondrial outer membrane permeabilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...histone H2AXY142 phosphatase activity / mesodermal cell fate specification / anatomical structure development / striated muscle tissue development / mitochondrial outer membrane permeabilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell differentiation / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jung, S.K. / Jeong, D.G. / Ryu, S.E. / Kim, S.J. | ||||||
![]() | ![]() Title: Crystal structure of ED-Eya2: insight into dual roles as a protein tyrosine phosphatase and a transcription factor Authors: Jung, S.K. / Jeong, D.G. / Chung, S.J. / Kim, J.H. / Park, B.C. / Tonks, N.K. / Ryu, S.E. / Kim, S.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 213.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 171.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 501.7 KB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hb1C ![]() 3gebS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31068.354 Da / Num. of mol.: 4 / Fragment: Eya domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q86U84, UniProt: O00167*PLUS, protein-tyrosine-phosphatase #2: Chemical | ChemComp-BEF / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.89 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.4M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 69154 / Num. obs: 68947 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Rsym value: 0.074 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 6733 / Num. unique obs: 6842 / Rsym value: 0.386 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GEB Resolution: 2.5→40 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
|