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- PDB-4v31: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v31 | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Deoxyuridine | ||||||
![]() | CEREBLON ISOFORM 4 | ||||||
![]() | SIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
![]() | ![]() Title: Thalidomide Mimics Uridine Binding to an Aromatic Cage in Cereblon. Authors: Hartmann, M.D. / Boichenko, I. / Coles, M. / Zanini, F. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 114.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.4 KB | Display | ![]() |
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Full document | ![]() | 477.3 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 13703.577 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MSR-1 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FLC / | #5: 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 % / Description: NONE |
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Crystal grow | Details: 0.1 M CITRIC ACID PH 3.5, 25 %(W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.4 Å / Num. obs: 28709 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.87 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.71 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.33 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→37.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.823 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 29.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.41 Å
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Refine LS restraints |
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