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Yorodumi- PDB-4v2z: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v2z | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pomalidomide | ||||||
Components | CEREBLON ISOFORM 4 | ||||||
Keywords | SIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE / CC-4047 / POMALYST | ||||||
Function / homology | Peptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / CULT domain / CULT domain profile. / Beta Complex / Mainly Beta / metal ion binding / S-Pomalidomide / Cereblon isoform 4 Function and homology information | ||||||
Biological species | MAGNETOSPIRILLUM GRYPHISWALDENSE (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2014 Title: Thalidomide Mimics Uridine Binding to an Aromatic Cage in Cereblon. Authors: Hartmann, M.D. / Boichenko, I. / Coles, M. / Zanini, F. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v2z.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2z.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2z ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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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) Strain: MSR-1 / 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 % / Description: NONE |
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Crystal grow | 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 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.3 Å / Num. obs: 54054 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.32 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.45 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.45→37.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.346 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.069 / 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 mean: 24.957 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→37.35 Å
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