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Yorodumi- PDB-7ps9: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ps9 | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220) | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / PROTEIN DEGRADATION / Immunomodulatory imide drug / E3 LIGASE | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / Chem-8W7 / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Heim, C. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system. Authors: Heim, C. / Hartmann, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ps9.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ps9.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ps9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/7ps9 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7ps9 | HTTPS FTP |
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-Related structure data
Related structure data | 7psoC 4v2yS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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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.) Magnetospirillum gryphiswaldense (magnetotactic) Gene: MGR_0879 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4TVL0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M (NH4)H2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.76 Å / Num. obs: 27318 / % possible obs: 97.7 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.141 / Net I/σ(I): 11.24 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 11 % / Rmerge(I) obs: 1.542 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4220 / CC1/2: 0.845 / Rrim(I) all: 1.611 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4v2y Resolution: 1.8→34.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.021 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 147.23 Å2 / Biso mean: 37.589 Å2 / Biso min: 21.5 Å2
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Refinement step | Cycle: final / Resolution: 1.8→34.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.844 Å / Rfactor Rfree error: 0
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