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Yorodumi- PDB-5oh2: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oh2 | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam) | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | UNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / pyrrolidin-2-one / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Boichenko, I. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D. | ||||||
Citation | Journal: Acs Omega / Year: 2018 Title: Chemical Ligand Space of Cereblon. Authors: Boichenko, I. / Bar, K. / Deiss, S. / Heim, C. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / 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 | 5oh2.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oh2.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 5oh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oh2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5oh2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5oh2_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5oh2_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/5oh2 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5oh2 | HTTPS FTP |
-Related structure data
Related structure data | 5oh1C 5oh3C 5oh4C 5oh7C 5oh8C 5oh9C 5ohaC 5ohbC 2v2y 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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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: 13703.577 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 (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: 1.8 Å3/Da / Density % sol: 30 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.4 Å / Num. obs: 24410 / % possible obs: 98.4 % / Redundancy: 2.86 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 3836 / CC1/2: 0.79 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V2Y 2v2y Resolution: 1.9→37.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.031 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.146 / 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: 41.434 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→37.4 Å
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Refine LS restraints |
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