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Yorodumi- PDB-5lp0: CRYSTAL STRUCTURE OF THE ZEBRA FISH ENTH DOMAIN FROM EPSIN1 IN 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lp0 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE ZEBRA FISH ENTH DOMAIN FROM EPSIN1 IN 1.41 ANGSTROM RESOLUTION | |||||||||
Components | Epsin 1 | |||||||||
Keywords | SIGNALING PROTEIN / ALPHA-HELIX / INTRACELLULAR MEMBRANE TRAFFICKING / ENDOCYTOSIS MEMBRANE ASSEMBLY / UBIQUITIN-BINDING PROTEIN | |||||||||
Function / homology | Function and homology information clathrin vesicle coat / clathrin binding / phospholipid binding / endocytosis / endosome / intracellular membrane-bounded organelle / plasma membrane Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | |||||||||
Authors | Levin-Kravets, O. / Prag, G. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: Nat.Methods / Year: 2016 Title: A bacterial genetic selection system for ubiquitylation cascade discovery. Authors: Levin-Kravets, O. / Tanner, N. / Shohat, N. / Attali, I. / Keren-Kaplan, T. / Shusterman, A. / Artzi, S. / Varvak, A. / Reshef, Y. / Shi, X. / Zucker, O. / Baram, T. / Katina, C. / Pilzer, I. ...Authors: Levin-Kravets, O. / Tanner, N. / Shohat, N. / Attali, I. / Keren-Kaplan, T. / Shusterman, A. / Artzi, S. / Varvak, A. / Reshef, Y. / Shi, X. / Zucker, O. / Baram, T. / Katina, C. / Pilzer, I. / Ben-Aroya, S. / Prag, G. #1: Journal: J.Cell Biol. / Year: 2000 Title: Epsin 1 Undergoes Nucleocytosolic Shuttling And Its Eps15 Interactor Nh(2)-Terminal Homology (Enth) Domain, Structurally Similar To Armadillo And Heat Repeats, Interacts With The Transcription ...Title: Epsin 1 Undergoes Nucleocytosolic Shuttling And Its Eps15 Interactor Nh(2)-Terminal Homology (Enth) Domain, Structurally Similar To Armadillo And Heat Repeats, Interacts With The Transcription Factor Promyelocytic Leukemia Zn(2)+ Finger Protein (Plzf). Authors: Hyman, J. / Chen, H. / Di Fiore, P.P. / De Camilli, P. / Brunger, A.T. #2: Journal: Nature / Year: 2002 Title: Curvature Of Clathrin-Coated Pits Driven By Epsin. Authors: Ford, M.G. / Mills, I.G. / Peter, B.J. / Vallis, Y. / Praefcke, G.J. / Evans, P.R. / Mcmahon, H.T. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lp0.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lp0.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lp0_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 5lp0_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 5lp0_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 5lp0_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lp0 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lp0 | HTTPS FTP |
-Related structure data
Related structure data | 5lozC 1h0aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 16767.115 Da / Num. of mol.: 4 / Fragment: ENTH DOMAIN RESIDUES 18-157 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: epn1 / Plasmid: PGST P.2 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: F1Q523, UniProt: F1Q5Z9*PLUS #2: Chemical | #3: 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: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 19% (W/V) PEG 3350, 0.1M POTASSIUM PHOSPHATE MONOBASIC MONOHYDRATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97881 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97881 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→62.788 Å / Num. obs: 95136 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.41→1.46 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H0A Resolution: 1.41→40.49 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→40.49 Å
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Refine LS restraints |
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LS refinement shell |
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