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Yorodumi- PDB-7pjk: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pjk | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / THALIDOMIDE ANALOGUES | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense MSR-1 (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Heim, C. / Hartmann, M.D. / Maiwald, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2022 Title: Replacing the phthalimide core in thalidomide with benzotriazole. Authors: Krasavin, M. / Bubyrev, A. / Kazantsev, A. / Heim, C. / Maiwald, S. / Zhukovsky, D. / Dar'in, D. / Hartmann, M.D. / Bunev, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pjk.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pjk.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 7pjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/7pjk ftp://data.pdbj.org/pub/pdb/validation_reports/pj/7pjk | HTTPS FTP |
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-Related structure data
Related structure data | 4v2yS 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: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 19 - 123 / Label seq-ID: 20 - 124
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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 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: 1.81 Å3/Da / Density % sol: 32.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M (NH4)2HPO4 |
-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 EIGER2 X 16M / Detector: PIXEL / Date: May 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→35.44 Å / Num. obs: 21052 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 13 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 3305 / CC1/2: 0.583 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4v2y Resolution: 1.99→35.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.789 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.17 / 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 max: 118.06 Å2 / Biso mean: 51.966 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 1.99→35.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3065 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.99→2.041 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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