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- PDB-5ohb: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ohb | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidin-2-one (Valerolactam) | ||||||
![]() | Cereblon isoform 4 | ||||||
![]() | UNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / piperidin-2-one / Cereblon isoform 4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boichenko, I. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D. | ||||||
![]() | ![]() Title: Chemical Ligand Space of Cereblon. Authors: Boichenko, I. / Bar, K. / Deiss, S. / Heim, C. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / 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 | ![]() | 142.2 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oh1C ![]() 5oh2C ![]() 5oh3C ![]() 5oh4C ![]() 5oh7C ![]() 5oh8C ![]() 5oh9C ![]() 5ohaC ![]() 4v2yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13703.577 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MGR_0879 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 30 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.2 Å / Num. obs: 33597 / % possible obs: 99.2 % / Redundancy: 3.23 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 5247 / CC1/2: 0.84 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4V2Y Resolution: 1.7→37.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.562 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.105 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.226 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→37.2 Å
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Refine LS restraints |
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