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Yorodumi- PDB-5amj: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5amj | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash II structure | ||||||
Components | CEREBLON ISOFORM 4 | ||||||
Keywords | SIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / PHOSPHATE ION / Cereblon isoform 4 Function and homology information | ||||||
Biological species | MAGNETOSPIRILLUM GRYPHISWALDENSE (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural Dynamics of the Cereblon Ligand Binding Domain. Authors: Hartmann, M.D. / Boichenko, I. / Coles, M. / 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 | 5amj.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amj.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 5amj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amj ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amj | HTTPS FTP |
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-Related structure data
Related structure data | 5amhC 5amiC 5amkC 4v2yS C: citing same article (ref.) 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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-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: Chemical | ChemComp-PO4 / #5: 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: 100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE |
-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: Feb 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→37.2 Å / Num. obs: 30163 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.86 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.79 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.16 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V2Y Resolution: 1.75→37.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.556 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / 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: 31.362 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→37.24 Å
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