+Open data
-Basic information
Entry | Database: PDB / ID: 3egb | ||||||
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Title | Structure of Pellino2 FHA domain at 3.3 Angstroms resolution. | ||||||
Components | Protein pellino homolog 2 | ||||||
Keywords | PROTEIN BINDING / Pellino / FHA Domain / E3 ubiquitin ligase / substrate binding domain / Phosphoprotein | ||||||
Function / homology | Function and homology information regulation of Toll signaling pathway / ubiquitin-ubiquitin ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade ...regulation of Toll signaling pathway / ubiquitin-ubiquitin ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å | ||||||
Authors | Ferguson, K.M. / Lin, C. / Schmitz, K.R. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Pellino proteins contain a cryptic FHA domain that mediates interaction with phosphorylated IRAK1. Authors: Lin, C.C. / Huoh, Y.S. / Schmitz, K.R. / Jensen, L.E. / Ferguson, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3egb.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3egb.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 3egb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3egb_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 3egb_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 3egb_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 3egb_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3egb ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3egb | HTTPS FTP |
-Related structure data
Related structure data | 3egaSC 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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Unit cell |
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-Components
#1: Protein | Mass: 31410.199 Da / Num. of mol.: 2 / Fragment: UNP residues 7-289,FHA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PELI2 / Plasmid: pET28 derivative (HTUA) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HAT8 |
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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: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 295 K / pH: 5.5 Details: 0.05 M sodium citrate, 23% w/v PEG 3350 MME, 1 M NaCl, pH 5.5, vapor diffusion, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→41 Å / Num. obs: 8337 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 19 |
Reflection shell | Resolution: 3.25→3.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.5 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EGA Resolution: 3.25→41 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.823 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.291 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.334 Å / Total num. of bins used: 20
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