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Yorodumi- PDB-7pso: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pso | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Avadomide (CC-122) | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / Immunomodulatory imide drug / UBIQUITIN LIGASE / PROTEIN DEGRADATION | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / Chem-835 / S-Thalidomide / PHOSPHATE ION / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 | 7pso.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pso.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/7pso ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7pso | HTTPS FTP |
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-Related structure data
Related structure data | 7ps9C 4v2yS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 3 molecules ABC
#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 |
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-Non-polymers , 5 types, 190 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-835 / ( | #6: Water | ChemComp-HOH / | |
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-Details
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: 1.84 Å3/Da / Density % sol: 33.11 % |
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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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 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: 1.52→44.24 Å / Num. obs: 47297 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 12 % / Rmerge(I) obs: 1.337 / Num. unique obs: 7506 / CC1/2: 0.783 / Rrim(I) all: 1.392 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4v2y Resolution: 1.52→44.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.878 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / 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: 91.16 Å2 / Biso mean: 28.883 Å2 / Biso min: 15.24 Å2
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Refinement step | Cycle: final / Resolution: 1.52→44.24 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: 1.52→1.557 Å / Rfactor Rfree error: 0
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