+Open data
-Basic information
Entry | Database: PDB / ID: 3n0a | ||||||
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Title | Crystal structure of auxilin (40-400) | ||||||
Components | Tyrosine-protein phosphatase auxilin | ||||||
Keywords | HYDROLASE / phosphatase-like domain / C2 domain | ||||||
Function / homology | Function and homology information synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / clathrin-dependent endocytosis / clathrin binding / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / SH3 domain binding / presynapse ...synaptic vesicle uncoating / clathrin heavy chain binding / clathrin coat disassembly / clathrin-dependent endocytosis / clathrin binding / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / SH3 domain binding / presynapse / vesicle / postsynaptic density / molecular adaptor activity / protein domain specific binding / intracellular membrane-bounded organelle / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Harrison, S.C. / Guan, R. / Dai, H. / Kirchhausen, T. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structure of the PTEN-like Region of Auxilin, a Detector of Clathrin-Coated Vesicle Budding. Authors: Guan, R. / Han, D. / Harrison, S.C. / Kirchhausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n0a.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n0a.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n0a ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n0a | HTTPS FTP |
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-Related structure data
Related structure data | 1d5rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41444.547 Da / Num. of mol.: 1 / Fragment: UNP residues 40-400 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: DNAJC6 / References: UniProt: Q27974, protein-tyrosine-phosphatase | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15.5% PEG 4000, 0.1 M HEPES, pH 7.5, 0.01 M CaCl2, 0.8 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2008 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→50 Å / Num. obs: 29000 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D5R Resolution: 2.2→33.9 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.492 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→33.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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