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Yorodumi- PDB-6r1d: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r1d | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / Chem-JP5 / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense MSR-1 (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Heim, C. / Hartmann, M.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives. Authors: Heim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / 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 | 6r1d.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r1d.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 6r1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/6r1d ftp://data.pdbj.org/pub/pdb/validation_reports/r1/6r1d | HTTPS FTP |
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-Related structure data
Related structure data | 6r0qC 6r0sC 6r0uC 6r0vC 6r11C 6r12C 6r13C 6r18C 6r19C 6r1aC 6r1cC 6r1kC 6r1wC 6r1xC 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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1 |
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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: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 20 - 123 / Label seq-ID: 21 - 124
NCS ensembles :
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-Components
#1: Protein | Mass: 13703.577 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic) Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 1.79 Å3/Da / Density % sol: 31.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG 6K, 5 % Glycerol |
-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: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→39.2 Å / Num. obs: 77977 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.67 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.64 / Num. unique obs: 12046 / CC1/2: 0.92 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4v2y Resolution: 1.1→39.2 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.922 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / 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: 17.049 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→39.2 Å
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Refine LS restraints |
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