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Yorodumi- PDB-2v24: Structure of the human SPRY domain-containing SOCS box protein SSB-4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v24 | ||||||
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Title | Structure of the human SPRY domain-containing SOCS box protein SSB-4 | ||||||
Components | SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4 | ||||||
Keywords | PROTEIN BINDING / PROTEIN-BINDING | ||||||
Function / homology | Function and homology information positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination ...positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / intracellular signal transduction / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Uppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. ...Uppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural Basis for Par-4 Recognition by the Spry Domain-and Socs Box-Containing Proteins Spsb1, Spsb2, and Spsb4. Authors: Filippakopoulos, P. / Low, A. / Sharpe, T.D. / Uppenberg, J. / Yao, S. / Kuang, Z. / Savitsky, P. / Lewis, R.S. / Nicholson, S.E. / Norton, R.S. / Bullock, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v24.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v24.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v24 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v24 | HTTPS FTP |
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-Related structure data
Related structure data | 2jk9C 3emwC 3f2oC 2fnjS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22756.725 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q96A44 |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST TWO RESIDUES REMAIN FROM A CLEAVED HIS6 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 6.5 Details: 0.1 M NACACOD PH6.5, 14.4% PEG10K, 0.16 M CAAC2, 20% GLYCEROL, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2007 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.1 Å / Num. obs: 13208 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FNJ Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.377 / SU ML: 0.212 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.209 / 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: 23.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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