brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / Nuclear events mediated by NFE2L2 / autolysosome / temperature homeostasis / endosomal transport / immune system process / intracellular non-membrane-bounded organelle / mitophagy / Signaling by ALK fusions and activated point mutants / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NRIF signals cell death from the nucleus / molecular condensate scaffold activity / NF-kB is activated and signals survival / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function
Sequestosome-1 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain ...EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62
Mass: 5841.748 Da / Num. of mol.: 1 / Fragment: ZZ-TYPE RESIDUES 120-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q13501
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.278 Å / Relative weight: 1
Reflection
Resolution: 1.41→50 Å / Num. obs: 107631 / % possible obs: 98.4 % / Redundancy: 13.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.063 / Net I/σ(I): 83.2
Reflection shell
Resolution: 1.41→1.43 Å / CC1/2: 0.985
-
Processing
Software
Name
Version
Classification
PHENIX
(1.11_2567)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.412→29.579 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.39 Details: Some reflections were omitted or filtered out for refinement due to higher redundancy.
Rfactor
Num. reflection
% reflection
Rfree
0.1646
815
10.01 %
Rwork
0.1356
-
-
obs
0.1386
8141
98.74 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 1.412→29.579 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
396
0
20
107
523
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
453
X-RAY DIFFRACTION
f_angle_d
0.811
617
X-RAY DIFFRACTION
f_dihedral_angle_d
17.254
258
X-RAY DIFFRACTION
f_chiral_restr
0.077
65
X-RAY DIFFRACTION
f_plane_restr
0.008
84
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.4124-1.5009
0.1854
128
0.1469
1155
X-RAY DIFFRACTION
95
1.5009-1.6167
0.174
139
0.1386
1247
X-RAY DIFFRACTION
100
1.6167-1.7794
0.1858
135
0.1328
1215
X-RAY DIFFRACTION
100
1.7794-2.0368
0.1617
136
0.138
1230
X-RAY DIFFRACTION
100
2.0368-2.566
0.1608
139
0.1383
1239
X-RAY DIFFRACTION
100
2.566-29.5853
0.1548
138
0.1305
1240
X-RAY DIFFRACTION
97
+
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