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Yorodumi- PDB-6dn6: SPRY domain-containing SOCS box protein 2 complexed with INNN(ABU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dn6 | |||||||||
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Title | SPRY domain-containing SOCS box protein 2 complexed with INNN(ABU) cyclic peptide inhibitor | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / proteasomal degradation / nitric oxide / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex | |||||||||
Function / homology | Function and homology information SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / 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 / Resolution: 1.59 Å | |||||||||
Authors | Law, R.H.P. / Caradoc-Davies, T.T. / Norton, R.S. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent. Authors: Sadek, M.M. / Barlow, N. / Leung, E.W.W. / Williams-Noonan, B.J. / Yap, B.K. / Shariff, F.M. / Caradoc-Davies, T.T. / Nicholson, S.E. / Chalmers, D.K. / Thompson, P.E. / Law, R.H.P. / 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 | 6dn6.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dn6.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/6dn6 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dn6 | HTTPS FTP |
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-Related 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: 23849.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q99619 |
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#2: Protein/peptide | |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M CHES, 20% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2017 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→42.5 Å / Num. obs: 29881 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 18.42 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.59→1.68 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.2 / Rpim(I) all: 0.241 |
-Processing
Software |
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Refinement | Resolution: 1.59→42.46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.079
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Displacement parameters | Biso mean: 20.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.59→42.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.65 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 2.795 Å / Origin y: -0.5804 Å / Origin z: -8.968 Å
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Refinement TLS group | Selection details: { A|* } |