+Open data
-Basic information
Entry | Database: PDB / ID: 5j45 | ||||||
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Title | Crystal structure of Shrub, fly ortholog of SNF7/CHMP4B | ||||||
Components | GH13992p | ||||||
Keywords | TRANSPORT PROTEIN / ESCRT / polymerization / membrane | ||||||
Function / homology | Function and homology information Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / fusome / Macroautophagy / contractile ring / female germ-line stem cell asymmetric division / ESCRT III complex / proximal dendrite / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway ...Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / fusome / Macroautophagy / contractile ring / female germ-line stem cell asymmetric division / ESCRT III complex / proximal dendrite / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / dendrite morphogenesis / neuron remodeling / mitotic cytokinesis / multivesicular body / cytoplasmic side of plasma membrane / autophagy / midbody / symbiont entry into host cell / neuronal cell body Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.758 Å | ||||||
Authors | McMillan, B.J. / Blacklow, S.C. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Electrostatic Interactions between Elongated Monomers Drive Filamentation of Drosophila Shrub, a Metazoan ESCRT-III Protein. Authors: McMillan, B.J. / Tibbe, C. / Jeon, H. / Drabek, A.A. / Klein, T. / Blacklow, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j45.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j45.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 5j45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j45_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 5j45_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 5j45_validation.xml.gz | 6 KB | Display | |
Data in CIF | 5j45_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j45 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j45 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14754.847 Da / Num. of mol.: 1 / Fragment: UNP residues 18-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: shrb, Vps32, CG8055, Dmel_CG8055 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 PLysS / References: UniProt: Q8T0Q4 |
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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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% v/v PEG10K, 0.1 M NH4CH3CO2, and 100 mM Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.758→50 Å / Num. obs: 3869 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 85.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9 |
Reflection shell | Highest resolution: 2.758 Å |
-Processing
Software |
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Refinement | Resolution: 2.758→43.578 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.758→43.578 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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