+Open data
-Basic information
Entry | Database: PDB / ID: 1k2f | ||||||
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Title | siah, Seven In Absentia Homolog | ||||||
Components | siah-1A protein | ||||||
Keywords | LIGASE / PROTEIN BINDING / beta-sandwich | ||||||
Function / homology | Function and homology information Antigen processing: Ubiquitination & Proteasome degradation / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / SCF ubiquitin ligase complex / male meiosis I / regulation of multicellular organism growth / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / post-embryonic development / protein catabolic process ...Antigen processing: Ubiquitination & Proteasome degradation / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / SCF ubiquitin ligase complex / male meiosis I / regulation of multicellular organism growth / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / post-embryonic development / protein catabolic process / protein destabilization / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / disordered domain specific binding / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / cell differentiation / protein ubiquitination / early endosome / positive regulation of apoptotic process / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.6 Å | ||||||
Authors | Polekhina, G. / House, C.M. / Traficante, N. / Mackay, J.P. / Relaix, F. / Sassoon, D.A. / Parker, M.W. / Bowtell, D.D.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-alpha signaling. Authors: Polekhina, G. / House, C.M. / Traficante, N. / Mackay, J.P. / Relaix, F. / Sassoon, D.A. / Parker, M.W. / Bowtell, D.D. #1: Journal: DEVELOPMENT / Year: 1993 Title: Isolation and characterisation of murine homologues of the Drosophila seven inabsentia gene (sina) Authors: Della, N.G. / Senior, P.V. / Bowtell, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k2f.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2f.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 1k2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2f ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 21423.533 Da / Num. of mol.: 2 / Fragment: C-terminal domain (residues 93-282) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pMalC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61092 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BME / #4: 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: 2.31 Å3/Da / Density % sol: 46.75 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: calcium chloride, ethanol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 13, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 12661 / Num. obs: 12661 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 64.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4.31 / Num. unique all: 1244 / Rsym value: 0.388 / % possible all: 99.4 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.7 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.228 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 56.7 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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