+Open data
-Basic information
Entry | Database: PDB / ID: 4z4m | ||||||
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Title | Crystal structure of GFP-TAX1BP1 UBZ2 domain fusion protein | ||||||
Components | Green fluorescent protein,Tax1-binding protein 1 | ||||||
Keywords | Flurorescent Protein / Metal Binding Protein / GFP / TAX1BP1 / UBZ / Zinc-finger | ||||||
Function / homology | Function and homology information protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / bioluminescence / generation of precursor metabolites and energy / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling ...protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / bioluminescence / generation of precursor metabolites and energy / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / kinase binding / autophagy / protein-macromolecule adaptor activity / cytoplasmic vesicle / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Rohaim, A. / Kawasaki, M. / Wakatsuki, S. | ||||||
Citation | Journal: Febs J. / Year: 2016 Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z4m.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z4m.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 4z4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z4m_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 4z4m_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 4z4m_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4z4m_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/4z4m ftp://data.pdbj.org/pub/pdb/validation_reports/z4/4z4m | HTTPS FTP |
-Related structure data
Related structure data | 3vhsC 3vhtC 3wupC 4z4kC 1emaS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 29589.242 Da / Num. of mol.: 2 / Fragment: UBZ2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human) Gene: GFP, TAX1BP1, T6BP, PRO0105 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: Q86VP1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.4 Details: 0.2 M Ammonium fluoride, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→63.87 Å / Num. obs: 30758 / % possible obs: 97.3 % / Redundancy: 8.6 % / Net I/σ(I): 6.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMA Resolution: 2.15→63.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.26 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.256 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.342 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→63.87 Å
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Refine LS restraints |
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