+Open data
-Basic information
Entry | Database: PDB / ID: 3geb | ||||||
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Title | Crystal Structure of edeya2 | ||||||
Components | Eyes absent homolog 2 | ||||||
Keywords | HYDROLASE / Activator / Alternative splicing / Cytoplasm / Developmental protein / Magnesium / Nucleus / Polymorphism / Protein phosphatase / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / extrinsic apoptotic signaling pathway in absence of ligand / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / extrinsic apoptotic signaling pathway in absence of ligand / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kim, S.J. | ||||||
Citation | Journal: To be Published Title: Structure of edeya2 Authors: Kim, S.J. / Jeong, D.G. / Jung, S.K. / Seong, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3geb.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3geb.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 3geb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3geb_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 3geb_full_validation.pdf.gz | 497.4 KB | Display | |
Data in XML | 3geb_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 3geb_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3geb ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3geb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31054.330 Da / Num. of mol.: 4 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O00167, protein-tyrosine-phosphatase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2006 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→50 Å / Num. all: 77791 / Num. obs: 76896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6.9 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11332 / Rsym value: 0.293 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The crystal form is twinned by the operator h,-k,-l, twinning fraction 0.35
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Displacement parameters | Biso mean: 41.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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