+Open data
-Basic information
Entry | Database: PDB / ID: 3g9h | ||||||
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Title | Crystal structure of the C-terminal mu homology domain of Syp1 | ||||||
Components | Suppressor of yeast profilin deletion | ||||||
Keywords | ENDOCYTOSIS / Syp1 / mu / adaptor / Phosphoprotein | ||||||
Function / homology | Function and homology information endocytic patch / Syp1 complex / mating projection base / Clathrin-mediated endocytosis / budding cell bud growth / septin cytoskeleton organization / cellular bud neck septin ring / unidimensional cell growth / actin cortical patch assembly / prospore membrane ...endocytic patch / Syp1 complex / mating projection base / Clathrin-mediated endocytosis / budding cell bud growth / septin cytoskeleton organization / cellular bud neck septin ring / unidimensional cell growth / actin cortical patch assembly / prospore membrane / cellular bud tip / cellular bud neck / mating projection tip / enzyme inhibitor activity / cell division site / positive regulation of endocytosis / endocytic vesicle / endocytosis / cell cycle / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Reider, A. / Barker, S. / Mishra, S. / Im, Y.J. / Maldonado-Baez, L. / Hurley, J. / Traub, L. / Wendland, B. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Syp1 is a conserved endocytic adaptor that contains domains involved in cargo selection and membrane tubulation. Authors: Reider, A. / Barker, S.L. / Mishra, S.K. / Im, Y.J. / Maldonado-Baez, L. / Hurley, J.H. / Traub, L.M. / Wendland, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g9h.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9h.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9h ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35691.230 Da / Num. of mol.: 1 Fragment: The C-terminal MU Homology domain, residues 566-870 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SYP1, YCR030C, YCR30C/YCR29C / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25623 |
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#2: Chemical | ChemComp-1PG / |
#3: 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: 3.41 Å3/Da / Density % sol: 63.88 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 30% PEG-400, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 13031 / Num. obs: 12752 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 13.9 % / Biso Wilson estimate: 73.3 Å2 / Rsym value: 0.092 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 7 / Num. unique all: 662 / Rsym value: 0.372 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→49.35 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1805404.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.5686 Å2 / ksol: 0.326643 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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