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Yorodumi- PDB-6r1x: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r1x | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7a | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation / hydrolysis product | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / Chem-JPQ / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense MSR-1 (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 6r1x.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r1x.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r1x_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 6r1x_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 6r1x_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6r1x_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/6r1x ftp://data.pdbj.org/pub/pdb/validation_reports/r1/6r1x | HTTPS FTP |
-Related structure data
Related structure data | 6r0qC 6r0sC 6r0uC 6r0vC 6r11C 6r12C 6r13C 6r18C 6r19C 6r1aC 6r1cC 6r1dC 6r1kC 6r1wC 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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3 |
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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: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 20 - 122 / Label seq-ID: 21 - 123
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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.) 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 grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Ammonium phosphate |
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-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: Apr 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.03 Å / Num. obs: 28238 / % possible obs: 99.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.12 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 4404 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.517 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / 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: 37.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.03 Å
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Refine LS restraints |
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