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Yorodumi- PDB-3ek9: SPRY Domain-containing SOCS Box Protein 2: Crystal Structure and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ek9 | ||||||
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Title | SPRY Domain-containing SOCS Box Protein 2: Crystal Structure and Residues Critical for Protein Binding | ||||||
Components | SPRY domain-containing SOCS box protein 2 | ||||||
Keywords | PROTEIN BINDING / SPRY domain / Ubl conjugation pathway / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / intracellular signal transduction / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kuang, Z. / Yao, S. / Xu, Y. / Garrett, T.J.P. / Norton, R.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: SPRY domain-containing SOCS box protein 2: crystal structure and residues critical for protein binding. Authors: Kuang, Z. / Yao, S. / Xu, Y. / Lewis, R.S. / Low, A. / Masters, S.L. / Willson, T.A. / Kolesnik, T.B. / Nicholson, S.E. / Garrett, T.J. / Norton, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ek9.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ek9.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ek9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ek9 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ek9 | HTTPS FTP |
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-Related structure data
Related structure data | 2fnjS 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: 23365.156 Da / Num. of mol.: 1 / Fragment: B30.2/SPRY domain residues 12-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spsb2, Grcc9, Ssb2 / Production host: Escherichia coli (E. coli) / References: UniProt: O88838 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 100mM Bis-Tris, pH6.5, 200mM MgCl2, 25% PEG3350, EVAPORATION, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 13, 2007 / Details: AXCO |
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→30.7 Å / Num. all: 5018 / Num. obs: 5002 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.117 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.2 / Num. unique all: 493 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FNJ Resolution: 2.6→30.69 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.833 / SU B: 12.125 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 17.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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