[English] 日本語
Yorodumi- PDB-3d8e: Crystal structure of the human Fe65-PTB1 domain (trigonal crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d8e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human Fe65-PTB1 domain (trigonal crystal form) | ||||||
Components | Amyloid beta A4 precursor protein-binding family B member 1 | ||||||
Keywords | PROTEIN BINDING / alpha-beta structure / phosphotyrosine binding domain | ||||||
Function / homology | Function and homology information negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization ...negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / amyloid-beta binding / growth cone / histone binding / transcription coactivator activity / molecular adaptor activity / nuclear speck / positive regulation of apoptotic process / synapse / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Radzimanowski, J. / Ravaud, S. / Sinning, I. / Wild, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structure of the human Fe65-PTB1 domain. Authors: Radzimanowski, J. / Ravaud, S. / Schlesinger, S. / Koch, J. / Beyreuther, K. / Sinning, I. / Wild, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain. Authors: Radzimanowski, J. / Ravaud, S. / Beyreuther, K. / Sinning, I. / Wild, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3d8e.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3d8e.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d8e ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d8e | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16782.211 Da / Num. of mol.: 4 / Fragment: Phosphotyrosine binding domain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65, RIR / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O00213 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 100mM HEPES, 5% (v/v) ethylene glycol, 10% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.0723 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→72.9 Å / Num. obs: 15431 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 16.209 / SU ML: 0.329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 59.775 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.396 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
|