+Open data
-Basic information
Entry | Database: PDB / ID: 3hb0 | ||||||
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Title | Structure of edeya2 complexed with bef3 | ||||||
Components | Eyes absent homolog 2 (Drosophila) | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase | ||||||
Function / homology | Function and homology information 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 / positive regulation of DNA repair / extrinsic apoptotic signaling pathway in absence of ligand / 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 / 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: 2.5 Å | ||||||
Authors | Jung, S.K. / Jeong, D.G. / Ryu, S.E. / Kim, S.J. | ||||||
Citation | Journal: Faseb J. / Year: 2010 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hb0.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hb0.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hb0_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
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Full document | 3hb0_full_validation.pdf.gz | 501.7 KB | Display | |
Data in XML | 3hb0_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 3hb0_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hb0 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hb0 | HTTPS FTP |
-Related structure data
Related structure data | 3hb1C 3gebS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 31068.354 Da / Num. of mol.: 4 / Fragment: Eya domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: Q86U84, UniProt: O00167*PLUS, protein-tyrosine-phosphatase #2: Chemical | ChemComp-BEF / #3: Chemical | ChemComp-MG / #4: 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: 69.89 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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