+Open data
-Basic information
Entry | Database: PDB / ID: 5onf | ||||||
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Title | The ENTH domain from epsin-1 | ||||||
Components | Epsin-1 | ||||||
Keywords | ENDOCYTOSIS / adaptor protein complex | ||||||
Function / homology | Function and homology information Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / clathrin binding / ubiquitin binding / actin filament organization / phospholipid binding ...Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / clathrin binding / ubiquitin binding / actin filament organization / phospholipid binding / endocytosis / early endosome / endosome / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Garcia-Alai, M. / GIeras, A. / Meijers, R. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Epsin and Sla2 form assemblies through phospholipid interfaces. Authors: Garcia-Alai, M.M. / Heidemann, J. / Skruzny, M. / Gieras, A. / Mertens, H.D.T. / Svergun, D.I. / Kaksonen, M. / Uetrecht, C. / Meijers, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5onf.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5onf.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 5onf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5onf ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 18005.471 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: ENT1, YDL161W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12518 #2: Chemical | ChemComp-MPD / ( | |
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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: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M CaCl2, 25 % PEG 3350 and 0.1 M Tris pH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.127 Å | ||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2010 | ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.75→27 Å / Num. obs: 13379 / % possible obs: 99.1 % / Redundancy: 5.3 % / Net I/σ(I): 11.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 28.878 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.471 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→27.11 Å
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Refine LS restraints |
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