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- PDB-8bc6: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bc6 | |||||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide | |||||||||
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![]() | SIGNALING PROTEIN / Protein Damage / Protein Ageing / Protein Chain Break / Aspartimide | |||||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / PHOSPHATE ION / Cereblon isoform 4![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Heim, C. / Hartmann, M.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon. Authors: Heim, C. / Spring, A.K. / Kirchgassner, S. / Schwarzer, D. / Hartmann, M.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.4 KB | Display | ![]() |
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Full document | ![]() | 480.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bc7C ![]() 4v2yS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13632.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MGR_0879 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 501.556 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The last residue is a cyclized asparagine, which is called aminosuccinimide, or more commonly aspartimide Source: (synth.) ![]() #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.5 M (NH4)H2PO4 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.718→37.23 Å / Num. obs: 32513 / % possible obs: 99.6 % / Redundancy: 12.73 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 12.46 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 5140 / CC1/2: 0.632 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4V2Y Resolution: 1.72→37.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.727 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / 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: 37.924 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→37.23 Å
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Refine LS restraints |
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